By the end of the year it is rather substantial (several thousand $) and I want to expense it correctly. What expense category would it fall under?
Based on your facts, I assume you receive a form 1099-MISC from the various companies you perform work for.
If the above is correct, then when you complete your Schedule C, just put those fees under miscellaneous expense and title them "submission fees".
They did not send a 1099-misc. The company is known for doing tricky work around. Like instead of paying me $10 less for the job they pay me $10 more and then charge me $10 to submit it. I have records of the payments. I assume I would do miscelaneous expenses.
whether you received a 1099-misc or not , you still enter the details as if you had received a 1099-misc ( to the extent feasible ) --- you tell TurboTax that you have self-employment income, then fill ( Schedule-C-EZ ) out the details of the category code, business name etct. etc. , then enter the gross income reported on 1099-misc and those not reported on 1099-misc, thewn you will come to the entering of expenses -- follow through instruction by instruction and you will be done. Note that your rental property income and expenses are reported on Schedul-E
Hope this helps -- if not tell me what more help you need