Is working for a company whose manager practices financial corruption, such as seizing bonuses, partnering with subcontractors, and increasing quantities of work items for his own benefit, considered a sin or participation in theft on the part of an employee who does not participate in these actions?

There is no sin in the questioner's mere employment in this company, nor any participation in theft, as long as he does not directly engage in any of the transgressions committed by his manager. Rather, his duty is to advise his manager and forbid him from this evil. If the manager does not respond, he should report the matter to the company owner or those in charge of it, provided he does not fear harm befalling him as a result.