I had office flow questions before I opened in September. My comments probably won't help much with your question though.

I don't use the financial parts of AC at all. After reading here and other places and talking to a few docs I decided to try Office Alley's online practice management. It's free and not bad for a small office like mine, although it is not very intuitive navigating through their system. We do some double entry of patient demographics in AC and OA, which would slow down a large, busy office.

I am a solo FP with one multifunctional employee who is my chaperone, medical assistant, biller, receptionist, etc.

Here's my office flow once a patient is in the office:
1. Patient calls for an appointment and my employee quickly collects all demographic information including insurance numbers. She then verifies their benefits before their appointment. The patient visits my website to fill out medical history forms.
2. Patient arrives, checks in, signs a few forms, copay is collected, insurance card and ID are scanned, and encounter form is printed with documentation of payment, and given to me on a clipboard. If the patient and employee have done everything right, a new patient spends less than 5 minutes in the waiting room.
3. I see the patient and document the visit in AC. I jot down the ht/wt and maybe a few vitals on the encounter form. I also jot down the ICD and circle the appropriate CPTs. Personally, I like to have some paper trail in the event of an electronic catastrophe or if a patient visit note "disappears" (which occurs more than I would like.)
4. I walk the patient back up to the front and give them their prescriptions. I give the encounter form back to my employee who posts all the info into OA at this time and submits the claim.