Is the salary earned from the company considered unlawful and does it affect the acceptance of supplications and good deeds, given that money was taken from the employer without his knowledge with the intention of repaying it in installments, and does this apply to those whom he supports with his money?

Taking money from a company without its owner's knowledge is a grave sin and a breach of trust (amanah (definition)). The money must be returned immediately if possible, or in installments, with this documented in your will. This money is ill-gotten (suht) and unlawful to consume if your family knows its true nature. However, your salary for permissible work is lawful and unrelated to the money taken through betrayal. Sincere repentance erases sins, for "the one who repents from a sin is like one who never sinned."