1. Do I have to calculate this money that I took without his knowledge and give it in charity on behalf of my father?
2. Or should I calculate this money and use it to pay off my father's debt, because he died when he was in debt?
3. Or should I regard it as something taken towards my wages, and I don't have to do anything?.
If the matter is as you described, and there was an agreement between you and your father that you would work for him in return for payment that was not paid in full, and you did not give up this right to him, and what you took from his wealth without his knowledge was no more than that, then you do not have to do anything.
This issue is similar to what was mentioned by the scholars with regard to the issue of zafar (lit. attainment), i.e., when a man takes a right to which he is entitled that he could not get directly.
Al-Shanqeeti (may Allah have mercy on him) said: If someone wrongs you by taking something that belongs to you in an unlawful manner and you cannot prove it, and you had the opportunity to taek something from him equivalent to what he took from you in such a way that you will be safe from accusation or punishment, can you take the equivalent of what you are entitled to or not?
The more correct of the two scholarly opinions and the most in harmony with the apparent meaning of the texts and analogy is that you may take the equivalent of what you are entitled to and no more, because Allah says (interpretation of the meaning): “then punish them with the like of that with which you were afflicted” [al-Nahl 16:126] and “transgress likewise against him” [al-Baqarah 2:194]. Among those who held this view were Ibn Sireen, Ibraheem al-Nakha’i, Sufyaan, Muhaajid and others.
A number of scholars, including Maalik, said that this is not permissible and that was the view of Khaleel ibn Ishaaq in his Mukhtasar, when he said concerning an item entrusted to somebody: He does not have the right to take from it something commensurate with the degree to which the person wronged him. Those who held this view quoted as evidence for that the hadeeth “Render back the trust to the one who entrusted it to you and do not betray the one who betrayed you.” End quote.
Even if we assume that this hadeeth is saheeh, it cannot be quoted as evidence in this case, because the one who takes the equivalent of what was his due and no more than that has not betrayed the one who betrayed him; rather he has settled the score with the one who wronged him. End quote from Adwa’ al-Bayaan, 3/353.
This has been explained in the answer to question number 27068.
You should have asked your father for your salary and not resorted to taking from his wealth without his knowledge, unless he refused to give it to you.
If it turns out that you took more than your salary from his wealth, then you have to return the additional amount to his estate, which includes paying off debts. There is no point in giving it in charity on behalf of your father.
Similarly, the one who takes wealth from someone else has to give it back to him if he is alive and to his heirs if he is dead, and he should not give it in charity on his behalf except if he is unable to find him or his heirs.
And Allah knows best.