Thanks Kelly & Guillermo for your responses.
@Kelly - No, unfortunately we do have to use Standard value allocation since the destination is basically a billing table that has actual invoice amounts.
@Guillermo Cuadrado - Formula would have been ideal. I tried modifying the SOURCE x Destination.Column formula a lot, but couldn't get to it. I finally appended Cost Source (General Ledger) to a Custom object (with a filter), and also appended the invoices table to it. Grouped it on amount, did a pivot, and subtracted both amounts to find the offset amount that I wanted to allocate. I then did another standard value allocation to this new custom object. So earlier my custom tower was over-allocating. Now, it's allocating 100%.
Thanks,
Jaison
#CostingStandard(CT-Foundation)