Hi Doug
This is not going to take your breath away, but what I do is give the deposit's check number a prefix such as DEP (e.g. DEP-12345), and then use GridView or Crystal to create a custom Aged Receivable report which excludes the DEP transactions (the report can't be easily backdated).
If desired, I will create another GridView which lists only unapplied DEP transactions, and use the total to make a GL journal entry adjusting the AR and Customer Deposits accounts (automatically reversed next fiscal period). By doing this, the custom report total should tie to the AR account balance.
This doesn't solve the problem of having to match the deposit against the invoice - if the billing module is set up so that the invoice number is NOT automatically assigned, then often the person entering the cash will know what the future invoice number will be and can "apply" the deposit to that invoice number, so that subsequent matching is unnecessary.
Steve