I'll go through my most recent setup. Maybe it'll give you some ideas of your own.
I have a 480 rad up top and a 360 on the floor of my case, both facing in an up/down orientation (as opposed to side-to-side). So what I've done for fill and drain ports is to use the top-facing ports in the top rad as fill ports, and a bottom-facing port on the bottom rad as a drain.
I had to drill holes for the top-facing fill ports from the top rad, but they get covered up out-of-sight when the top panel/ filter-cover is snapped back onto the case. The way it worked out is better than I expected. I can fill my entire loop in one go with only the tiniest bit of trapped air left to bleed out. I'll first open up both fill ports in the top rad, one to add a funnel to fill and the other one to let air out so an air bubble won't get stuck over on that side of the rad, and then before I start filling I'll crack open slightly the fill port in my tube res just to let air escape from it as I fill the loop from the top rad, and I'll close the fill port on the res when the water has filled up into it to the very top and then I'll continue filling up the rest of the loop until the top rad is full.
An added benefit of using the two top-facing ports from my rad as fillports is it gave me an excellent / easy place to screw in a schrader valve and an air gauge so I can air-pressure leak test my loop prior to filling with any liquids. Sure beats putting down paper towels and crossing my fingers I don't have a leak.
As far as the drain port goes I just have an end-plug capped mini-valve into a 90 degree rotary in one of the bottom ports on the rad. It points towards the back (right) side of the case out of view unless I take the right-side panel off. I just make sure the valve is closed, unscrew the end cap and screw into it a barb with a short piece of hose pointed towards a jug/bucket, open the fill-ports to let air in, and crack open the valve to let it drain.
Aaaaand, if I get impatient I have a drill-pump I can hook to my drain port and using a cordless drill it'll drain the entire loop in about 30 seconds, more-or-less.
Another cool thing I should mention about the drill pump (besides the fact that it's cheap - as long as you already have a drill) is that, unlike watercooling pumps, it's self-priming, which means it doesn't need water to feed into the pump. It creates a suction that can pull water through the hose to the pump. That way it helps get out little pockets of water that otherwise usually stay trapped in the loop, and that helps reduce/eliminate dribble when disassembling components from the loop.Edited by Unicr0nhunter - 3/4/14 at 2:21pm