So you want to split the loop but with a shared res? In effect its still just one giant loop, as the water temperature will equalize anyway, so, at best, you may gain some performance from pushing more restriction into one loop and having a faster flowing CPU loop (ala the Typhoon III res), however, this will be countered by having a more complex tubing run.
In short, I believe you should either go 2 full loops (ie completely separate), or just one large loop. I kind of like the one large loop idea, as I tend to either use lots of CPU, or a little CPU and lots of GPU (most games are still single threaded, so can only push your CPU so much).
Of course, the best way... is to test both and see which works best for you
(and I'm not 100% sure I understand what you are suggesting).