I'll throw my 2 cents into this... Let me start with my setup involved drilling 6 holes in the back of a glass tank so this may not be the route you want to go.
I am using a 4 port Oceans Motions to control the direction of flow in the tank. I have a Dart pump to drive the flow.
I drilled four holes along the bottom of the back as entry points for the CL. Each hole being the output of one of the ports on the Oceans Motions. There are two holes in the middle of the back (one on the right and one on the left side) that are in intake to the Dart.
Here's a picture to help...
I then built a frame work out of PVC pipe for my rock to sit on top of to keep it off the bottom glass. This frame has 4 seperate "sections"; each section connected to one of the holes in the back of the tank. These sections then have one or two loc-lines to direct the flow as needed.
A so-so picture showing the PVC frame
A picture of the Oceans Motions plumbing project
And finally a picture with sand over the frame
This setup worked well for me because of the aquascape I wanted to do with two islands and an arch... Probably wouldnt work for other people. As you can see in this picture you don't really see any of the loc-line after the rock was put in place.
My inspiration for this type of setup came from Steve Weast's plumbing designs; if you would like some more to look at
http://www.oregonreef.com