He stole from the company he used to work for, then he repented, but he has some questions
Question

                I used to work for a company and made lots of profit for the company. The boss promised me bonus but kept delaying the bonus due to which i stole from them.He broke the promise due to which i got angry and stole more than what i deserved. Since i no longer work there i have decided to return to my knowledge. I do not remember exact amount.

1. I have returned half of the amount through a friend of mine. This friend still works at the same company. The owner entered into a contract agreement with my friend for opening a new business. Since my friend did not have enough amount to pay the owner as part of his contract agreement i decided to help my friend but at the same time return owner his amount. Please tell me if this was ok as i have returned half the stolen money plus helped my friend.

2. The other half im still trying to return in other ways w/o telling the owner but my full intention is to return them.During this time are my prayers + duas accepted because i read the repentance is not fulfilled until stolen amount is returned completely.

3. There are somethings i bought from the stolen money but i have donated to the poor people but i will repay the amount to the owner completely. Is this acceptable.

Please tell me if i can seek istikhara prayer to return the amount in the easiest way possible. Are my good deeds accepted in the mean time or not like prayers, zakat, zikr.
Praise be to Allah.
    Firstly: 

    Stealing is a major sin, and we praise Allah for having 
    guided and enabled you to repent. So strive hard to make sure that your 
    repentance is as prescribed in Islam, and do not respond to evil with evil, 
    or find false excuses based on misinterpretation. The fact that your boss 
    broke his promise to you does not justify your stealing and continuing in 
    it, especially since you state that he only did that because of what you 
    stole from them. 

    Secondly: 

    You should try hard to find out how much you stole from the 
    company. If you are not able to find out exactly how much it was, then work 
    out what you think you most likely took from them unlawfully, then return it 
    to them. Allah, may He be glorified and exalted, says (interpretation of the 
    meaning): “So keep your duty to Allah and fear Him as much as you can” 
    [at-Taghaabun 64:16]. 

    Shaykh as-Sa‘di (may Allah have mercy on him) said: 

    This verse indicates that if a person is unable to do an 
    obligatory deed then it is waived in his case; if he is able to do some of 
    what is enjoined and unable to do some of it, then he should do what he is 
    able to do, and what he is unable to do is waived in his case. The Prophet 
    (blessings and peace of Allah be upon him) said: “Whatever I instruct you to 
    do, do as much of it as you can.” This Islamic principle covers innumerable 
    minor issues.

    End quote from Tafseer as-Sa‘di (p. 868). 

    Thirdly: 

    As you have returned half of what you took from the company 
    unlawfully, you have done well, and you should strive hard to return the 
    other half. 

    You do not have to inform the owner of the company of the 
    situation or of what you have done, or of what you intend to do, if you fear 
    that this will result in bad consequences or fitnah, or if it is difficult 
    for you to tell him and you are afraid that there may be some negative 
    consequences for yourself, because Allah loves to conceal people’s faults. 
    Rather what you must do is restore rights to those to whom they belong, no 
    matter how that is done, so long as it is permissible; then you must repent 
    to Allah, may He be glorified and exalted, and ask a great deal for 
    forgiveness. 

    Please see the answer to questions no. 
    31234 and 43017 

    Fourthly: 

    Righteous deeds such as praying, fasting, giving charity, 
    offering supplication (du‘aa’), remembering Allah (dhikr), and so on, with 
    the intention of repentance and striving to restore people’s rights, will be 
    accepted in sha Allah. In fact they are part of repentance as enjoined. For 
    a righteous deed to be accepted, it is not essential that the doer should 
    have no sin, major or minor, on his record, and committing a major sin does 
    not necessarily erase what the doer has to his credit of righteous deeds, 
    unless that pertains to a particular case concerning which there is a text. 

    Rather confusion may arise concerning acts of worship that 
    are connected to that sin; in such cases the sin will have an impact on the 
    acceptability of the deed, and may cause it to be rejected and not 
    accepted. 

    This case is similar to the case of repentance from sin 
    whilst persisting in other sins. 

    Ibn al-Qayyim (may Allah have mercy on him) said: 

    Is repentance valid if one repents from one sin whilst 
    persisting in another sin? That is a matter concerning which there are two 
    scholarly opinions … My view concerning this matter is that repentance from 
    one sin cannot be valid when one is persisting in another sin of the same 
    type. But in the case of repenting from one sin when still committing 
    another that has nothing to do with it and is not of the same type, that 
    repentance is valid. For example if a person repents from dealing in riba 
    but has not repented from drinking alcohol, for example, his repentance from 
    riba is valid. But if a person repents from dealing in riba al-fadl (when 
    similar commodities are exchanged unequally, such as one measure of dates 
    for two measures of a different quality of dates) but he does not repent 
    from riba an-nasee’ah (when the amount of debt is increased when the debtor 
    is unable to pay off the debt at the appointed time and requests extra time 
    in which to pay it off), and he persists in it, or vice versa; or he repents 
    from smoking hashish but persists in drinking alcohol, or vice versa – in 
    such cases his repentance is not valid. This is like one who repents from 
    committing zina with one woman but is still committing zina with another 
    woman and has not repented from that; or he has repented from drinking wine 
    but he is still drinking other intoxicating drinks. In such cases he has not 
    really repented from sin; rather he has merely moved from one type to 
    another. This is unlike one who turns from one sin to another that is of a 
    different type.

    End quote from Madaarij as-Saalikeen (1/273-375) 

    Fifthly: 

    With regard to these things that you bought with that stolen 
    money and gave in charity to the poor, you should understand that your 
    giving these things in charity to the poor is not valid, regardless of 
    whether you gave the items themselves or the amount for which you bought 
    them, because that is haram wealth that must be returned to its rightful 
    owners. It is not permissible to give it in charity because Allah is Good 
    and does not accept anything but that which is good. 

    As you intend to return the money in full to its owners, then 
    you have done well, and you should hasten to return it. 

    Sixthly: 

    It is not prescribed for you to pray istikhaarah about 
    returning this wealth to its owners, and you do not need to do this prayer 
    with regard to the possible way of returning it, because returning it when 
    you are able to do so is obligatory, and it is not prescribed to pray 
    istikhaarah about something that is obligatory. Shaykh Ibn ‘Uthaymeen (may 
    Allah have mercy on him) said: One should not pray istikhaarah about 
    something that is obligatory, because Allah has ordained that it is 
    obligatory.

    End quote from al-Liqa’ ash-Shahri (4/135). 

    See also the answer to question no. 11981

    But if you are hesitant about two possible ways of returning 
    it, and you do not know which of them is better and closer to concealment, 
    then istikhaarah may be appropriate, because you are uncertain as to the 
    choice between two things that are prescribed, and you cannot work out which 
    of them is better. 

    And Allah knows best.