how can you tell what piston rod goes to the cap?

you should have marked the caps when you took then off .did you put new rod bearings in it if so did you plastigauge them to check the clearance?

YOU NEED TO MARK BEFORE TAKING APART YOU COULD CREATE OTHER ISSUES

You may now need to get an engine machine shop to recondition all the rods, this will include the caps! Is the crank in GOOD shape, if not suggest having it machined as well, if not done already. There will never be a better time to get this right!!