It usually is state and local that causes the biggest problems.

My fees weren't large at all. Probably only 300-400 bucks per year for the whole shootin match.
I used Quick Books Pro with a subscription.(had employees) All electronic. I shoot it to them every month, they do their thing, and shoot it back. Pretty simple. It did pretty much everything for me on a daily basis that I had to do.

We didn't do sales tax tho. All our customers were tax exempt under Industrial Processing.