AP invoice and payment integration with third party supplier

We are attempting to use a 3rd party supplier to automate AP and AP payments in Epicor. We are using DMT and have successfully created a combined AP entry template. The Payment entry using DMT is very difficult. Any ideas on how to make payment entry using DMT easier? We are currently using 2 separate template for payment entry Check Head and Payment entry. Our roadblocks are head number and check number.
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