I have two pumps that I mounted in the middle of my brutus-10 like sculpture. I've never had a problem with them clogging from hops or grains, but I also use a false bottom in the boil kettle that probably keeps the bulk of the matter out of the pump. My system is basically a HERMs setup, if I need both, one is usually pumping wort through the CFC and the other is running hot or cold water to change the temp of the wort, or into the mash for fly sparging while the other pump is slowly draining the mash tun.
I currently have the in and out sides mounted vertically only because they're too close to each other to mount horizontally - which I believe is the correct orientation for them ( you can unscrew the heads and mount them in 90 degree changes.) But I haven't had too many issues with this, I make sure I keep the pumps flushed between brews to avoid stuff growing in the bottom of the u-joint I made out of copper adapters with the QD attached.
While I've considered plumbing up the sculpture and have written up some initial plans for it, I let it go as I have other things to do and running the ins and outs using silicone tubing and a bunch of QD's (since I already have them) work just fine. I have probably 8 different length silicone tubes with QD of varying length depending on what's going where. It's not as snazzy as diverter valves going to a manifold kind of thing with copper running everywhere, but it works well enough for me.
where I mounted the pumps (basically two 1x2 rectangular SS tubing)http://temporal.shutdown.com/album/beer/slides/img_0904.jpg
(i've since switched to SS QD's, the CPC ones were causing me issues)