I use Quickbooks Pro for mine. So far I've had no issues. I run payroll on it, manage the IRS mandatory reports (941, TWC, etc). I keep up with AP, AR, expense reports, inventory.etc.
It has been user friendly. I do have an at home working mom who is a whiz in QB who "tutors" me when I need help on something. She gets me set up on everything. $85/hour and WELL worth it.
I don't know your business but we are in the consulting and raw materials industry and run it from home. We will eventually need to get an office due to the growth, we currently warehouse inventory in a couple places in TX.
I have a large 4 drawer file with extreme detailed files. I keep a handy file by my desk for the things I need on hand and quick such as filing away expense receipts, mileage reports, incoming invoices, IRS, etc.
My system is detailed to the extreme but I can locate a document within minutes. We also use Excel program to run an AP and AR to make sure we have everything up to par and that keeps track of vendors, trucking companies, etc.
I also have a large 5 subject notebook that I use as a check register for the 3 accounts we have with QB. I reconcile with my hand ledgers and bank daily and then reconcile via the bank statement and QB program once a month.
I realize I sound extreme about the books and I am but we own the company we are running revenue upwards of $3 million a year and it has to be right.
We are happy with QB. I back it up often, send a portable file to our accountant and he double checks to make sure I am on track.