Is there a problem with my work, which involves preparing technical and financial proposals for a company whose manager often wins bids through illicit means?

Your original work is permissible if the tasks submitted for bids are permissible. However, your manager's acquisition of bids through deceitful means is a Shariah violation, as it involves lying, deception, and bribery. You must enjoin your manager from these reprehensible acts. If he does not desist, you must leave working with him, because your continued presence assists him in sin, which is forbidden by Shariah, as Allah states: "And cooperate in righteousness and piety, but do not cooperate in sin and aggression."