I'm not sure what consistency or condition your old substrate is in, but as a rule of thumb when switching tanks you should try to use as much of the old rock and substrate as possible to maintain the biofiltration that the new tank will lack.
Even if you opt to cover the sand you have now with new "dead" sand or new live sand, it would be a good idea to keep some of it.
Never go barebottom in a reef, it will actually increase your nutrient problem...even shallow sand beds provide some denitrification.
You asked what to look for while doing this....you have it figured out when it comes to buckets, extra water, etc. I would suggest getting several 30 gallon rubbermaid containers at about $3 or $4 a piece...they wil make the operation easier. Someone suggested a kiddie pool so you can lay out all your rock and get a good feel for what you have and how you should set it up. Don't forget to take into account the hydrogen sulfide that may have built up under your sand bed in the last six months. To avoid killing anything with this "black sand" area that may have formed, you should take everything living out of the tank BEFORE attacking the substrate for removal. Then use a gravel vacume to suck out the black sand. If you don't see any darkened areas under the sand, then you don't have this problem.
Try to use as much of the old system water as possible by draining as much clean water out of the tank before you start kicking up dust moving things.
Good Luck