I'm just an ordinary QBO user, not QBO professional, however I went through the exact set of questions you're asking, and there is no good news. There is no acceptable workflow IMO.  You basically have undo the voided entry and then create a journal entry or a bank deposit for the debit to your checking when the deposit from bill.com posts. 

The implementation is nothing short of horrible.  It's useless.  We stopped using it. 

Sorry there's not better news.