I did something similar with
my res . My bleed fill lines connect to the res. The res is a PVC T fitting. The josnson pump is connected to the side outlet. The top line is the air/water exit. 1 of the lower lines is a fill tube while th other 2 are just returns.
If I flush the system with a soap mixture some will run out but most will run through the system. It takes about 2 minutes of running water through the fill tube and letting water out of the escape tube to get all the soap out. It also makes flushing the air out of the system pretty easy as the escaping water carries out.
My point though is the water gets pretty well mixed in the res. The only problem I'd see in using a secondary cooling loop would be the fact you could never get the coolant to ambient. However I could see using a secondary loop for use with some kind of filter.