I tried a few different ways to do partial payments, however could not figure one out.
In the end we changed our workflow and now take 100% up front in all cases rather than a 50% deposit. The result has been less work for staff and our bookkeeper, and we have not had any customer complaints about it.
One note: you can only put the paypal / stripe links on Sales Quote or Sales Invoice documents...not on Sales Order documents. I can't understand this logic.