I do my own bookkeeping but I have H&R Block do my income tax. I'd recommend Quickbooks. I use it and its well worth the money I invested in it. I was using the Quicken Home & Business but that didn't meet my needs after a while.
All manual transfer for me ... miva/quickbooks ... it is a pain.
I am probably looking for the same thing as you. I have multiple servers (some cpanel/whm, some plesk and some are a proprietary control panel ... so i cant use whmautopilot).
QuickBooks Pro. I import PayPal data (they export quickbooks files) and manually enter my CC processing info off the statement I get each month. I then enter in my business expenses each month and any affiliate commission checks I receive. If you link it to a bank account I'm sure it'd be even easier, but there's too much junk going in and out of mine to filter personal from business.