Don't think there's any easy way to do this and use the retention calculations in PCM.
I would suggest a) use line item retention calculation. b) create SOV line items, each with 10% retention. c) create an additional line item for the pre-payment amount (with zero retention) and status this as 100% complete. d) create one more line item equal to the prepayment amount as a NEGATIVE number with zero percent complete and zero percent retention.
This will show each line item for their full amount and show the pre-payment amount as this period, and the SOV will equal the correct amount. If you number this requisition 0000 then the first requisition will be 0001
In 0001, you status SOV lines with progress, which will calculate the retention amounts. On the second pre-payment line (the negative line) you would manually enter in "this period" a NEGATIVE amount equivalent to the total retainage on other line items, and also enter a NEGATIVE amount equivalent to the total retainage from other line items. This will demonstrate how much of the pre-payment is being used, and still keep the total "retainage" on the summary page at zero.
This would be a fair amount of manual effort, but would illustrate on the forms what you're doing, I think. You'll want to test this before you start submitting them.
The other way would be to do all of this calculating manually, use the "use summary amount" total and just type in the total retention on the summary page dollar amount each month.