About 12 years ago, I was working as a night auditor in a hotel, and I was responsible for all the money that the Hotel made every day. At that time my manager (owner) used to cheat on my paycheck by deducting some of my working hours as a way to pay me less money on my pay check.On the other hand, and because of his action I used to take some cash money from the Hotel account without his knowledge (I was stealing his money) as an action against him, but I was taking a lot more money than he took from me. I left that Hotel around 1992 when he sold the hotel and I left for a different country. After that I felt very guilty about what I had done. Now, after all these years, still feel very guilty about that action. I would like you to let me know what do I have to do now to let "Allah" forgive me for what I did? This owner is nowhere to be found now and that happened in the U.S.A.

Praise be to Allah, the Lord of the World; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.

No doubt, the behavior of the manager with you is forbidden. Despite his wrong doing you are not allowed to take more than your actual right from his money since it is a breach of trust which a Muslim is ordered to respect faithfully. The owner had trusted you when appointed you as an accountant in his hotel. So being disloyal to him means cheating him, deceiving him and exposing yourself to Allah's anger. Allah ordered us to be loyal Allah Says (interpretation of meaning): {O you who believe! Betray not Allâh and His Messenger, nor betray knowingly your Amânât (things entrusted to you, and all the duties which Allâh has ordained for you).} [8: 27].
Therefore, you have to make repentance; one of the conditions of a sincere repentance is giving back to people their rights. So, you have to try your best to give that person his money. If you cannot find him then you have to give it in charity. If you should meet the person after doing so, inform him that the money you took illegally from him was given in charity. If he does not approve of it you have to give him back his money and the reward of the charity would be yours, Insha Allah. Even if the person is not a Muslim you have to give that money to needy people with the intention of getting rid of money which does not belong to you.
Allah knows best.