All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
Just doubting the source of the money of your father and the probability that it could have been ill-gotten money is of no effect because in principle what a Muslim possesses is his property.
Shaykh Ibn Taymiyyah said: “In principle, what a Muslim has in hand is his property if he claims that it is his, therefore if it is not known from where he obtained the property that he has in hand, then one should apply this principle. Even if he had stolen that money while one does not know that, then what is not known is like what does not exist…. As regards a Muslim whose condition is unknown, then there is no doubt about (the permissibility of) his dealings in principle, and if one abandons dealing with him out of Wara’ (extreme piety), then he has indeed introduced an innovation for which Allaah has sent down no authority. So, if we look to a particular amount of money in the hand of a person and we do not know that it was taken unlawfully from someone else or obtained in a way that does not imply ownership, and we got it from him (in a lawful manner) or that we got it from him as a gift or as fees (for a service) or in return for a loan, then we are not sinful for that according to the agreement of the scholars .”
This means that if we do not know that a person takes ill-gotten money or that he is involved in that, then we should not doubt about him or avoid dealing with him as this is dispraised Tanattu’ (excessive contention).
As regards the issue of exchanging money, then it must be done actually, i.e. from hand to hand, or potentially like through a bank account (through which the purchased currency enters into the buyer’s account) or through a certified cheque and the like, for more benefit, please refer to Fataawa 129699 and 133410.
With regard to taking your wages as a percentage from the profit derived from the work if any, then this is not valid according to the view of the majority of the scholars because the amount of such wages is not known, whereas it must be defined, so it is not acceptable or valid to make it a percentage from an unknown amount.
Finally, we advise you to stay with your father in his company taking care of his employees whereby you advise them and admonish them in a soft and gentle manner.
Allaah Knows best.