Hi Joe - there's loads of help for all this stuff on CB's guides pages (via the ? top right of the screen).
All payments on account or overpayments, waiting to be allocated to customer invoices or suppler bills can be seen on the "unallocated cash" screen in the Money tab, so, once you have entered a bill from the supplier you can go there and allocate payments against it.
Alternatively, on the unpaid bills screen you can use the "Manage" drop down on the right hand side of the bill and then "Payment" OR can click on the bill and use the "Allocate payment" button, which takes you to the same place to allocate any unallocated payments.
Despite my comment about the guides, you have probably picked the most complicated and cumbersome feature of CB to ask about!