I created a subcontract, but I need to have a 5% of retainage, but the prepayment takes 5% too

The base documents (subcontract in your case) drives the line settings. I don’t think out of the box you be able to achieve what you need. Alternatively you can customize AP301000 to always display the Retainage tick mark and make the percentage editable for the lines. Although you may later experience difficulties when you exercise prepaids write off that I’m unsure about it.

Thank you so much aaghaei.