It makes very little sense you should write two checks one for rent less the 10% and one check to Marin County Tax Collector! He may be trying to show less in rent for an income property? I have no idea but I wouldn't do it.
Have a short term rental agreement drawn up showing what your rent is in total and a receipt showing that you paid your rent in full for that duration. He can write the tax collector himself, he's a grown up isn't he?