Don't have a Busellato, but our Masterwood has pop up pins. To align the front pins, I move them all forward about 2mm. Then trim a long part at Y=0, and while the vacuum is holding it down, align the pins to the part. This aligns the router spindle with the pins, then I start drilling holes and adjust the location parameters of the drilling spindles until everything is where it's supposed to be. On the masterwood I can adjust the stop location parameters on a zone by zone basis to get each zone to line up.
It's also extremely important that your parts are perfectly square when they come off your saw, or that will make it much more difficult to accurately dowel. We cut our wall cabinet sides a hair long and trim them on the pt to pt so that the bottoms are perfectly flush when doweling.