I set up as an S-Corp, but would do something simpler if I had to do it over.
I only use "Time & Materials contracts" because any other type allows government to open my books and inspect them. With T&M, the only thing they get to see is a timesheet. I record hours in Excel spreadsheet, and then once a month slip the hours into the spreadsheet template and pdf it over to my client. It takes about 5 minutes. When I have expenses, I bill them as materials (no markup).
For payroll, when I first started, I just used the small business payroll options through my bank, but because I only billed monthly, I kept having to re-learn what I was doing every month. After a few months, I also wanted to set up a 401K, and I used Paychex to do that, and for about $1200 year, they also did all my paycheck stuff including withholding, tax forms for fed and state, and my form 5500 (for when the 401k gets big enough). I still did all the timesheets and invoicing in Excel.
I did have a client demand worker's comp insurance once, and after paying for it for one year, in the second year, I told them I wasn't doing it anymore, showed them that it wasn't required for one-person companies (I can't sue myself) and they accepted it. I worked government contracts as a subcontractor, so my clients were used to the paperwork. But they were always surprised when I crossed things out or added things to their "standard contracts" haha. Always remember, a contract is simply an agreement between two parties. There's nothing "standard" that you cannot change.
I bought quickbooks when I first started contracting, and found it was overkill for what I wanted/needed. Excel worked just fine for me.