The Adagio Invoices module does invoicing for your Customers. This is different than logging the invoices that you receive from your Vendors. This would be entered in Adagio Payables, in an invoices batch.

Then you could use the steps that Doug outlined for generating the payment.

The webinar that Andrew mentioned would show the basics of where the important functions of Adagio Payables can be found. It's only an hour long and doesn't go into extreme detail on absolutely everything, but it's enough to get started.