IIRC, it should be in the Home>Setup page. Right in the middle of the screen is your choices: Auto, Input, SD Ref, HD Ref. Pressing the middle button of the cursor key should give you the flashing selector, move it over to what you want (SD Ref) and then press the middle button again. I'm not 100% on this, but pretty sure.
Thanks for the help. We are using the D5 deck in 720 mode which will only take a SD reference not Tri-sync, which is why we couldn't figure out how to make it switch. A bit confusing, but it was in the manual. If the deck is in 1080 it will accept Tri-sync as reference. Thanks again.