Is it permissible to work with what I have learned from computer programs that were trained on using unlicensed copies, and will a person be held accountable for whether the programs in his workplace are original or copied?

If you repent to Allah for your previous use of protected software, then there is no blame upon you for working with the experience you have gained. As for your second question, if you know that the software used by your employer is pirated, you must denounce it, because the Prophet (peace and blessings of Allah be upon him) said: "Whoever among you sees an evil, let him change it with his hand; if he cannot, then with his tongue; if he cannot, then with his heart—and that is the weakest of faith." You are not permitted to use this software in your work, as that constitutes an infringement upon people's property without right.