Are you tagging the invoices as paid from the holding account or just leaving them there until they’re cleared? Although it may be premature to mark them as paid from that account, it would certainly show you what’s tied up with each invoice.
It would be pretty much inline with my colleagues post:
So essentially, when you write the cheque, mark the invoice as paid from the holding account. Then when the funds leave your main bank account, tag it as a transfer. That way, each invoice is tagged and any without a cheque or a payment tagged to it will still be outstanding, and the holding account’s value will show you how much is pending clearance too.
Does that make sense? If not, I’ll mock up an example for you.