i guess if you use 2 completely different loops you can use different color dyes. If ti's like 2 pump and 2 resevoirs like you previously illustrated... that's not going to work. Also if you share the water like how you were originally thinking, you need to seriously think out the flow rates of the two loops. Otherwise the one with the faster flow rate will empty it's resevoir and you'll be stuck with a burned out pump.
Just a question about your initial thoughts, why 2 loops? I understand using 2 cores (to get rid of heat), but what you're doing with two loops you can do with one, with 2 cores. i'd think that just one pump should have enough pressure and flow to get all your components nice and cool. With you, aren't you just doing the same (with one or two loops) + you are added the heat from the second pump