We use one of the three (I believe), NY-Med Billing, and the process is fairly simple. We just batch the bills and send them out. The only problem is that there is apparently nothing to add a copay to until a bill is created. So I had to write a separate app to keep track of all patient payments (I'm sure there are other options), and I add the copays to the bills before they're batched and sent. But we are a very small practice, one solo Family Doc, and I could see how for a larger practice this could become burdensome.
It's not hard to reach the billers by email, and they usually reply promptly. You can write to me if you'd like further information at kurtkaufman at hotmail dot com.