First time Invoicing

We are preparing to run our first round of invoicing via Zoho this Friday. I have a couple of hopefully basic questions:

1. We have a number of pre-payments, which we entered into "Payments Received". Will those payments appear on the associated invoice so that amount due is adjusted accordingly?

2. We have outstanding amounts from some clients carrying over from July. What are some good ways to get that information included on the upcoming invoice?