This is a basic process in Dynamics GP and there are a couple of ways to manage check processing.
you can create a batch of invoices to pay based on various selection criteria that select invoice from your entire payables list. But you can also go vendor by vendor, and select the individual invoices you want to pay.
You can easily make partial payments on invoices if you want.
Any payment discounts that are assigned to an invoice will automatically be calculated and deducted from the payment.
The process for creating EFT files uses the same basic process.
This is a video that shows one way to put a check batch together: