I always put my foot braces in after the deck and hull are attached. I find it easy and I use an ocean cockpit whereas a regular large cockpit will even be easier. I use the height that commercial boats use and it seems to land right on my shear joint which in many ways is ideal since there is way more glass there. If you have another kayak that you use, life is easy as far as the length. Or sit against a wall and take measurements. I assume you mean commercially made foot braces with a track. I use Yakamas. Make a paper template of the track screw holes distance and don't rely on measuring. I put mine in so my ideal distance from the seated position puts them in the center of travel distance on the track so I can adjust them forward or back a bit (just in case). Two people make it easer if one e holds the track while the other drives in a screw. Don't crank it down until both screws are in.

I've done it myself by starting the first (closest one) screw myself and putting a bent piece of strip holding the track in position while I screwed in the other screw.