ideally you want them matched so they continue to wear at the same rate. new caps, or the same caps put in a different location, will see accelerated wear on the cap and the cam.
My F3 valve train was in buckets when i got it. My journals and caps were all just lightly worn. I fit them properly to the towers (look for the tapered end of the cap), and lubed them up well during assembly and break-in.