Ruling on building above or beneath a mosque
Question

                Before he died, my father instructed me to build a mosque with some of his money as an ongoing charity. It is to have a prayer room on the ground floor and above it a charitable medical centre and an institution for memorising Qur'aan, as well as an Islamic library and a private parking lot for visitors to the medical centre.

Is it permissible to build above and beneath the mosque or is it better to change the request and build the mosque on its own and have the rest of the charitable activities in a separate building?.
Praise be to Allah.
      Firstly: there is nothing wrong with having the mosque 
      beneath a structure or above it, if it is built in this manner from the 
      outset. 

    In al-Mawsoo‘ah al-Fiqhiyyah (12/295) it says: The 
    Shaafa‘is, Maalikis and Hanbalis regard it as permissible to make the top of 
    the building a mosque but not the bottom, or vice versa, because the two 
    structures are independents units that may be given as waqfs; therefore it 
    is permissible to give one of them as a waqf and not the other. End quote. 

    The scholars of the Standing Committee for Issuing Fatwas 
    were asked: I have built a house and my intention that was formed before 
    starting to build was to have a mosque beneath the house. The house has been 
    built and the qiblah has been determined, and the washrooms for the mosque 
    have been built. The carpentry work has been completed and there is nothing 
    left but painting; the mosque has been given an Islamic appearance. But I 
    heard from some people that building a mosque under the house is not 
    permissible. I stopped using the house and did not open the mosque for five 
    years until we find out what to do. What is your opinion about building the 
    mosque under the house? Please note that there are other small mosques that 
    have been built in the neighbourhood during this period and there are now 
    numerous small mosques. Please advise me, may Allah reward you with good. 

    They replied: There is no reason why the mosque cannot be 
    under the house if the mosque and the house were built from the outset in 
    this manner, or if the mosque is created in the structure beneath the house. 
    But if accommodation is built above the mosque at a later date, then this is 
    not permissible because the roof of the mosque and whatever is on it are 
    part of the mosque. End quote. 

    Fataawa al-Lajnah al-Daa’imah, 
    5/220, vol 2. 

    Secondly: 

    The basic principle is that bequests are to be carried out 
    and not changed so long as they do not involve any sin, because Allah says 
    (interpretation of the meaning): “Then whoever changes the bequest after 
    hearing it, the sin shall be on those who make the change. Truly, Allaah is 
    All-Hearer, All-Knower” [al-Baqarah 2:181]. With regard to changing them 
    to something better, there is a difference of scholarly opinion. 

    Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) said: 
    Changing the bequest to something better than it is a matter concerning 
    which the scholars differed. 

    Some of them said that it is not permissible, because of the 
    general meaning of the words of Allah (interpretation of the meaning): “Then 
    whoever changes the bequest after hearing it, …” [al-Baqarah 2:181]. And 
    no exception is made except in the case where the bequest involves sin; so 
    the matter should be left as it is and not changed. 

    Some of the scholars said: Rather it is permissible to change 
    it to something better, because the aim of the bequest is to draw close to 
    Allah, may He be glorified and exalted, and to benefit the recipient of the 
    bequest. So whatever brings a person closer to Allah and is more beneficial 
    to the recipient is what should be done. The one who left the bequest is a 
    human being who may not be aware of what is better, and what is better at 
    one particular time may be different from what is better at another time. 
    And because the Prophet (blessings and peace of Allah be upon him) permitted 
    changing vows to something better although it is obligatory to fulfil them. 

    What I think with regard to this matter is that if the 
    bequest is to a specific person, then it is not permissible to change it, 
    such as if the bequest is to Zayd only, or a waqf that is established to 
    benefit Zayd, then it is not permissible to change it because it is 
    connected to the rights of a specific individual. 

    But if the bequest is not made to any specific person – such 
    as if it is for mosques or for the poor – there is nothing wrong with 
    changing it for the better. 

    End quote from Tafseer al-Qur’aan by al-‘Uthaymeen, 
    4/256 

    Based on this, it is permissible to build the mosque on its 
    own and the other facilities separately, or it is permissible to put them 
    all in one building. 

    And Allah knows best.