Most that I've seen go bare bottom underneath and behind the rock. Then they put about 1/4" up front just to cover up the acrylic/glass bottom. This is what I do as well. Just put gravel where you are going to be able to clean the gravel.
In opposition to popular opinion, I am using about 4" of fine aragonite substrate. I've always run my tanks with substrate, and although it seems the majority no longer believes that this is a good thing, I've not had any problems in the last 7 years. Usually I've used a plenum beneath the sand, but in my latest tank I have just put the sand directly on the bottom.
As to whether the CC will crash the system, I'd have recommended a finer substrate, but given how often we reefers seem to upgrade or change our tanks I doubt the system will be running in this same configuration long enough to become a huge problem
I use to typically put about 1-2.5" sand in the bottom of mine. Though, I wish I had put more crushed coral in my 20 long just so I didn't need to have a frag cup in there all the time. It would have made fragging mushrooms a lot easier.
Saltfishlover- I am putting substrate only where it can be seen. I agree with plumberbob, I like BB under the rocks and a little sand upfront. This is coming from 3 years of a deep sand bed (DSB) in my reef tank.
For a tank that is going to house soft corals and zoo's a sand substraight is not a bad idea, soft corals need alot more nutrients for tissue build up then hard corals, a sand system actually buffers in the nutrient that are bound up in that sand so it can be a match made in heaven.