I have a ton of LR
in my system as a whole and when I do PWCs I remove water fromt the system out of the 55 so I suck any nasty stuff off the bottom of the tank. I have about 40lbs of LR
in there right now on the non-lighted side of the tank just because I have no where else for it to go.
What I have been doing is chipping the rock away under the colony taking a few polyps at a time. I like doing it this way because the polyps are attached to a bit of rock and it makes for an easier surface to glue them down to the plugs. A few of the frags in the tank I just set the plugs next to the colony and after a week or so they grew onto the plug. I have 28 different types of zoas in my tank so what you see in the frag tank is only a small slice of what I have. For some reason even the "slow" growers grow like weeds in my tank.
As for the plumbing its really simple I drilled the hole in the tank put a bulk head in and plumbed it into my return tank. I have a Mag5 as the return pump and it pulls water from the return tank (main system return) and puts it into the frag tank. My tanks are side by side.