Hi Warr - Many people these days seems to prefer to build a structure on which they tie their live rock to. This is elevated off the substrate..... The original/old school of thinking was to have the rock on the glass, and the sand around the live / base rock, that the sand engulves about the bottom 1 to 2cm (perhaps more) of the rocks....
The idea behind "elevated" rocks, is that detritus won't gather around the bottom of the rocks - between the rocks and the substrate....
So no real better way, If I elevate,how high ?
Good flow is all you need to flush out detritus and to allow flow around your rocks so as not to create to many dead spots. About 2- 4 cm should be fine.
Hi Warr - you can try and tie zoanthids or star polyps against the structure, and have the polyps cover the piping - alternatively, you can basically just wait that the corralline algae covers the piping..... Or, perhaps pack some very small pieces of live rock (live rock rubble) just in front of the piping to hide it - but then you might be back to square one...
Instead of using eggcrate, how about getting a piece of pipe about 20mm dia, then cutting it up into 15mm lengths and using them as pillars for your rock work, little bit of milliput (prattleys putty) on each, just to keep it still, and you will have much better flow under your rock, i find eggcrate eventually gets clogged with crap (i dunno, maybe i didn't use it properly??) but using small pillars gives less chance of detritus traps.
when your live rock is lifted of the sand it also creates more surface area, therefore more biological filtration.