I typically use a self-priming centrifugal pump (Berkley) with either a 40 gal or 80 gallon guzzler (whichever applies).
For very silty/muck bottom situations I put the guzzler inside a plastic garbage can. I typically use a pvc intake line and 45 at the end where the guzzler goes into the can. I rig the end so the guzzler stays put several inches off the bottom of the can.
It's actually pretty easy to float the intake line out to it's destination with this set up. Tip the intake line a little to introduce water into the can. It's not that hard to control the amount of water going into the can making it buoyant for you.
Once you've fed it out the entire length, tip the can a little more and the water will fill....it will sink and rest on the bottom right where you want it. The garbage can protects the filter from the bottom debris. It's a pretty simple, cheap and effective condom for your filter.
May sound hokey, but it's worked well for me.