Bill, unfortunately it does have to be done manually, but it can be done easily when you access each collection. Acquisitions using the TCDB transaction tool will always put the card into your Main Collection, so then you'll just go to your Pitcher's Batting PC and access the set and click on the button to add the card(s).
I want to say, though, that this is an excellent way to keep track of your collection. Back when I had multiple collections I ended up with lots of duplicates because I was stubborn and only wanted it posted in one collection. They way you're doing it will keep you from accumulating unwanted dupes. But again unfortunately you'll have to add them manually as you get them.
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“Aslan didn't tell Pole what would happen. He only told her what to do. That fellow will be the death of us once he's up, I shouldn't wonder. But that doesn't let us off following the signs.” - Puddleglum in The Silver Chair by C. S. Lewis