I've tried a couple different ways and a lot of it depends on where I have large decorations and such that may interfere with water circulation. I'm using these two configurations at the moment:
I prefer the first one as everything is on one side of the tank and on the back wall which makes it easy to hide with a single plant. The spraybar is not capped on one end so most of the water is sent to the other end of the tank and some of it towards the front glass. I prefer the water circulation in this setup because it's like a wirlpool and most of the waste deposits under the intake (prefilter).
The second seup has the spraybar on one side of the tank, great for hanging hornwart off of but the current in the opposite side of the tank tends to push the plants down and they end up growing sideways instead of straight up. I plan on changing this to get rid of the downward current on the left side. I think I will try placing the spraybar vertically along the back wall to try and get a similar effect as the first setup.
In both cases the spraybar is below the water line to reduce surface agitation. In the first setup, the spraybar has been cut in half to help hide it easier.
It's really up to you and I'm sure you will change it a couple of times until you are happy with it. In general however, place the intake as low as you can, most of the waste tends to sink and that's where you want to suck it in form. The output is usually towards the top to allow a little surface circulation/agitation, this helps reduce buildup of surface film.
Hope that helps