How do i categorize expenses in the software tool for things like irs fees, florida dept of state expense, and fees from freelancing sites like upwork?

What are IRS fees? You can't deduct Federal taxes paid as an expense. If your FDOR fee is for an Annual Report, then it is a miscellaneous expense with an explanation. Fees paid to freelance sites are miscellaneous expenses as well.

The IRS fees were what I had to pay for taxes last year. 

Yes, FDOR is an annual payment I make.

I'll add it and the freelancer fees to Miscellaneous.

Thank you for your reply.