Allocating a transferred payment in bank feeds

I've transferred a payment from my main bank account, into a holding account set up for a big client. (I needed to do this for a double payment & subsequent reversal...long story!).

So I make the transfer, then Take Payments using that customer holding account. The amounts match and I can reconcile them in that holding account.

The issue is the original payment into my main bank account remains Unallocated. How do I allocate it? I do have the option of Allocating to the holding account. But that seems like I'm doing the same thing twice, ie, Allocating AND transferring. Am I doing it correctly?