Just chiming in to say this is on our wishlist as well! As an association for educators, we have many members who are married couples that pay their dues together or sometimes parents who pay their dues as well as their child's student member dues. When they send us a check they expect to see a single charge for that amount in their bank account, not 2 separate charges that don't correlate to their records. We end up depositing the physical check and just "recording" it in YM, but of course that just delays it clearing on their end since we only do bank deposits a couple of times/month.
On a related note, we should be able to transfer a single invoice between profiles instead of only having the option to move all of them. There are times that dues are accidentally processed on the wrong profile (the couples situation mentioned above) and it would be much simpler to just transfer that transaction and adjust expiration dates manually than have to log into the payment processor to void/refund the transaction and do it all over again on the correct profile, not to mention the extra transactions on the customer end as a result.