Hello-
These are all good questions. I've only been in the billing bus. for 18mos. but here are my answers:
1. No, I do not charge a set up fee, however my contract with my clients states they give me 3 business days to learn their existing software (assuming they have any), and if necessary, to input provider and patient data into my own system.
2. Yes, I charge a monthly fee. It is a flat fee (the same every month) This fee is based upon many factors, such as # of claims each month, if they want me to post payments to their ledger, if they want me to send invoices to their cash customers w/ outstanding balances etc.
3. I always try to submit claims through the doctors own existing software. If they have none, I use Office Ally.
-Best of Luck