Is this a customer deposit?  If so, it sounds like you'd want to do is select a GL account (Customer Deposits) instead of an invoice, which is possible.  There's a line type to be selected.  This is a good thing to go through with your Sage partner, though, because of the ramifications of handling deposits one way over another, including through SO vs. AR.

If you're talking about a deposit you're making to a vendor, that too can be done a few ways. But here's one. https://help-sage100.na.sage.com/2019/Subsystems/AP/APMainProced/Record_a_Prepayment.htm