My setup is something like this:
I use the cintiq almost like an easel, keeping it very upright. It took me a while to get used to the angle and doing steady lines and stuff, but I prefer it this way because it keeps the strain off my neck/shoulders, since I'm sitting upright and not leaning over the tablet.
I keep my lighttable at a similar angle when drawing traditionally, and when I am using an actual easel for paintings, so it's something I'm fairly used to by now.