This should be your favorite part of using phpaga, and your favorite part of running your business! When you go to create an invoice you can do it with description/price line items or with tasks. Your choice. You may have to bill your client for equipment only one month, for that you would simple "Add invoice" not "Add invoice with Tasks".
When you get a check from a client, you want to let phpaga know about it. Click on "Invoices" under the FINANCE section, and click the invoice from the list, or do a search. The HTML detail page for the invoice will display, with a "Set Payment Date". Click the calendar button and select the date it was paid. This will update various graphs, and reports in phpaga, letting you know where your finances are.