Nan Even with a car the easiest route from Varenna to Bolzano would be to head back south to the A4 and then east to pick up the A22 north.
If you are thinking about going north from Varenna to SS39 and the fairly straight shot northern route, I'd suggest reconsidering. It will take you longer and it is mountains the whole way. Lovely scenery I am sure but two lanes and probably lots of switchbacks.
I once cut across from Ravenna to Florence on the little roads instead of going back to the autostrade. Forgot about that pesky little mountain range in the middle. When I got close Florence I called the hotel for directions, I had a hard time convincing them that I was really where I said I was. They kept saying nobody goes that way any more. :-)