One way to accomplish this is by using the "Draw" field in the AP Distribution line.  When you enter invoices from your subs, enter the "Draw" number that correlates to the draw number of your billing to the owner that reflects the subs charges.    

When you've been paid by the owner, in AP you can "Select Invoices for Payment" by displaying by job number and applying the condition "Draw = XXX" where XXX is the draw number you used when entering your sub invoices.

One way to accomplish this is by using the "Draw" field in the AP Distribution line.  When you enter invoices from your subs, enter the "Draw" number that correlates to the draw number of your billing to the owner that reflects the subs charges.    

When you've been paid by the owner, in AP you can "Select Invoices for Payment" by displaying by job number and applying the condition "Draw = XXX" where XXX is the draw number you used when entering your sub invoices.

You may also need to change some AP settings to display the "Draw" column for the Vendor Types used for your various subs.