Is money earned from working in a company whose manager resorts to forging invoices to pay less customs duties permissible or forbidden, and must one leave this company?

If your work at the company is not related to unlawful (haram) activities or fraud, then there is no objection to your salary. As for customs taxes, if the state takes them unjustly, there is no harm in evading them. However, if the state imposes them in exchange for services or to meet the needs of the nation, then it is not permissible to circumvent them, and concealing profits and falsifying prices is considered deception. In this case, it is not permissible to obey the company owner in committing fraud, and if one is compelled to do so, he must leave the job.