When you’re tagging a transfer between accounts the system gives you the option of either matching the transaction with one that it has found in the destination account, or it can create a new transaction in there.
Unfortunately there isn’t a way of doing this when using bank tagging rules, it can only be done manually.
It is actually not a fault. Only use the auto-feed for your current accounts, credit cards, merchant accounts and so on, but not for the holding accounts. Because most of the money going into the holding account comes from one of your other accounts (cash, current, …), and it is more or less the same for the money going out.
If you have feeds for all your other accounts, you can create auto rules (as you do already) for those accounts and almost all transactions from or to your holding account will be tagged from the other accounts via auto-rules, which will create the relevant entries in your holding account(s). You only have to enter entries like interests on your holding accounts or transfers between holding accounts or when you pay a supplier direct from a holding account. For that reason everything I pay or receive goes over my current or merchant account, even transfers between holding accounts go over the current account, because this way it will create all necessary entries via auto-rules, and I have no duplicates.
You could also keep the feed for your holding accounts on but then you have to delete the auto-tagging-rules, because it will create duplicates. When you tag the entries manually, lets they from your current account, quickfile will look in your holding account for matching entries and you just have to confirm it. The down side is you can not create auto-tagging-rules for this kind of tagging.
It is a little bit of a fault though because we should be able to make software do what suits us, not work around what suits the software. But hey, this will work for now