Like you said, it's silly to use ProSeries billing if your firm uses other accounting software.  We use Sage for our inhouse accounting software so that's what we use for billing purposes.  I too don't like Quickbooks, but we use it out of necessity because of the number of clients using it.  Using Quickbooks and using ProSeries is like inoculating yourself with a form of cancer since they intertwine with each other and just make our lives more difficult at times.