Hi Amorton,
Click this link to see the instructions from the Sage 100 Contractor online help system:
help-sage100contractor.na.sage.com/.../Sage100Contractor.htm

Process an electronic payment in AP. AP>Tasks>Process Manual/Quick Checks. In the drop down under payment type, choose EFT payment then choose the vendor and corresponing invoices that were paid. Process as you would a quick or manual check and this payment will then show up in your CM check register.

Anne - that's good information, but I think that is for 300 CRE and the question was regarding 100 Contractor 

Actually we are 300 CRE, i think I posted my question in the wrong spot. :)  Anne's answer will work perfectly for me!

Set them to pay as you would normally

Open 4-3-2

Select “record payment by”

Select online payment

Complete the pop up window

Use “online“ as transaction/check #