webpromo,
This is basically the same issue posted in http://forums.dotnetinvoice.com/forums/thread/316.aspx and http://forums.dotnetinvoice.com/forums/thread/170.aspx. This is still on our feature list, but it hasn't made it to the top yet. It will require a major overhaul of the way clients, payments, and invoices interact, so that is why we haven't added it as a quick fix at some point.
DotNetInvoice will accept your payment for $32 and then the invoice will show a positive balance of $0.25. One option would be to enter a payment of $31.75 on the existing invoice, and then generate the next invoice and add the $0.25 payment.
---
Jeremy
DotNetInvoice Support