Have you come across the
D-Plug fittings yet? Might mean you can pull the res off, fill it and put it back - obviously depends on whether there's going to be any flow (into the case!) while not there. If there is, QDCs would work but aren't cheap.
If you're talking about topping up, you should be able to top up anywhere and it'll find its own level. As you say, for starting up you'll need to fill both as you need both pumps fed with coolant - they don't like running dry. Alternatively, you could fill one and only run one pump. That would fill the other and probably the rest of the loop too. Worst case you flip-flop between which pump you're running....just try to stop the pump before it runs dry or you'll get air locks.
You could probably tidy things up a bit with thinner tubing - as long as it's about 10mm ID you're not going to see much of a gain going higher as G1/4 fittings have an ID just less than 10mm - and also fittings to make runs straighter. The thing is, with the number of runs you've got going on, you're going to be spending lots on fittings to do that and only you can decide whether it's worth it. If you're already thinking different case it sounds like it wouldn't be. If you have a look at some of the builds with Bitspower hardline and right-angles you'll see what I mean - it looks great but damn is it expensive!
when it comes to OCUK (must be all the haribos 
.
Some issue with the USB3 ports however which I'll need to look at. I've looked at the 1366 X58 Xeon 5650 thread where someone had this issue for years until they upgraded to a Xeon and realised their PCIe frequency was set to 101 mhz instead of 100 mhz! Or something to that effect.
