Is it permissible to take a percentage of the marketing funds allocated for advertisements, in exchange for expertise and knowledge, without harming the company's interest, given that one receives a small monthly salary?

It is not permissible to take anything from the company's funds without the permission of its owners, as that is treachery and consuming wealth unlawfully. Your entitlement to a higher salary does not justify treachery. Rather, you may ask the company owners for an increase, and if they refuse, you are free to leave them. It is not permissible to take a percentage of the funds without the permission of their owners, and this is forbidden even if you think you deserve more than what was agreed upon.