How to Bury the Deceased
Question

My father passed away recently whilst on Hajj.
In my tradition people come to pay condolences By saying sorry to her about your loss etc after which they ask everyone present to raise their hands and say Fatihah and maybe darud also.
From my knowledge I have heard that this may be a Bi`ah, and I took the general rule that whatever is in life is permissible unless it has been made prohibited and whatever is in the religion is prohibited unless it's been made permissible. Thus not knowing what one is supposed to do i tried my best to stay away from doing anything which i had no knowledge of ering the body and putting the soil
4 can one place a mark or name on a rock etc at the grave
5 And after completion of putting the soil what Du`a if any should one say (because even in jannat al mualla ,after we had buried my father the workers at the graveyard had one worker making Du`a with raised hands and the others saying amin, is this allowed?)
6 I also noticed whenever one visited a relative's grave an worker would ask which grave it was and would put a bucket of water on that grave. Is this allowed?
Praise be to Allah.Carrying the deceased and following the funeral
It is obligatory to carry the deceased and follow the funeral. This is one of the rights that the dead Muslim has over the Muslims, which will bring great reward and virtue to the one who does it. 
The Messenger of Allah (peace and blessings of Allah be upon him) said: “Whoever attends the funeral from the house (of the deceased) [according to one report: whoever follows the funeral of a Muslim out of faith and the hope of reward] until the funeral prayer is offered will have one Qirat, and whoever attends the funeral until the deceased is buried will have two Qirats.” He was asked, “O Messenger of Allah, what are the two Qirats?” He said, “Like two huge mountains.” (Narrated by Al-Bukhari, Al-Jana’iz, 1240).
It is not permitted to follow funerals in manners that go against the Shari`ah. That includes:

Crying or weeping in a loud voice; 
Following it with incense (Bukhur) etc.; 
Reciting Dhikr in a loud voice in front of the coffin as it is being carried, because that is Bid’ah. Qays ibn `Abbad (may Allah have mercy on him) said: “The companions of the Messenger of Allah (peace and blessings of Allah be upon him) used to regard it as disliked to raise the voice in front of the coffin” – and because it is an imitation of the Christians. 

How to bury the deceased in Islam
Muslims should not be buried with the disbelievers, nor the disbelievers with Muslims. The Muslim should be buried in the Muslim graveyard.  
The Sunnah is to put the deceased into the grave from the end, then he should be turned onto his right side in the grave, with his face directed towards the Qiblah . The one who puts him into the Lahd  should say, “Bismillahi wa ‘ala sunnat Rasul-Allahi or ‘ala millat Rasul-Allahi (peace and blessings of Allah be upon him) (In the name of Allah and according to the Sunnah of the Messenger of Allah or according to the religion of the Messenger of Allah (peace and blessings of Allah be upon him)).” (Narrated by At-Tirmidhi, Al-Jana’iz 967; classed as authentic by Al-Albani in Sahih Sunan Abu Dawud, 836) 
It is recommended for those who are at the grave to throw handfuls of earth, three handfuls scooped up in both hands, after the Lahd has been sealed.
What to do after the burial?
After the burial is complete, there are several things which are Sunnah: 

To make the grave a little higher than the ground, approximately a handspan, and not to make it level with the ground, so that it may be distinguished as a grave and respected, and not subjected to disrespect. It should be made approximately a handspan higher than the ground, and there is nothing wrong with placing a marker such as a stone or something similar, so that others of his family may be buried near him later on. Water should be sprinkled on the grave so that the soil will settle and not fly around.
No one should stand by the grave telling the deceased that he will be questioned soon etc., as is the custom among some people.
Rather people should stand at the grave and pray for the deceased to be made steadfast and for forgiveness for him. Those who are present should be told to do this, because of the Hadith of `Uthman ibn `Affan (may Allah be pleased with him), who said: “When the deceased had been buried, the Prophet (peace and blessings of Allah be upon him) would stand by (the grave) and say: ‘Pray for forgiveness for your brother and ask for him to be made steadfast, for even now he is being questioned .’” (Narrated by Abu Dawud, Al-Jana’iz, 2804; classed as authentic by Al-Albani in Sahih Sunan Abu Dawood, 2758) 
Nothing of the Quran should be recited at the graveside, because this is Bid`ah. The Prophet (peace and blessings of Allah be upon him) did not do this, and neither did his noble Companions. 
It is prohibited to build up graves or to plaster them or to write anything on them, because Jabir (may Allah be pleased with him) said: “The Messenger of Allah (peace and blessings of Allah be upon him) forbade us to plaster graves with gypsum, to sit on them or to build anything over them.” (Narrated by Muslim, Al-Jana’iz, 1610. According to Abu Dawud,  “He forbade us  to plaster graves with gypsum, to write on them or to step on them.” (Al-Jana’iz, 3226. Classed as authentic by Al-Albani in Sahih Sunan Abu Dawud, 2763) 

How to offer condolences in Islam
It is prescribed in Islam to offer condolences to the family of the deceased. This should take the form of whatever is thought will bring them consolation, stem their grief and help them to be patient. 
Condolences should be offered in the manner reported from the Prophet (peace and blessings of Allah be upon him) if one can remember that, otherwise use good words that come naturally which achieve the same purpose and align with Islamic principles. 
The Prophet (peace and blessings of Allah be upon him) said: “To Allah belongs that which He has taken and that which He gives, and with Him everything has an appointed end, so be patient and seek reward.” (Narrated by Al-Bukhari, Al-Jana’iz, 1204) 
What to avoid when offering condolences?
Two things must be avoided:

Gathering to offer condolences, even though the people do that.
The family of the deceased preparing food to offer to those who come to offer condolences.

The Sunnah is for the relatives and neighbours of the deceased to make food enough for the bereaved family. 
References:

Ahkam Al-Jana’iz by Al-Albani (may Allah have mercy on him).
Al-Mulakhkhas Al-Fiqhi by Al-Fawzan (213-216).

And Allah knows best.