During the cycle you will want to check Ammonia and Nitrites.
You will see the Ammonia go up first, then the Nitrites, then both of them drop back down to 0. When that happens your tank is cycled. Until then, you can pretty much skip all the other tests (well, except salinity). This will save on the chemical testing supplies
Don't think you would much heat issues, but depending on the strength of the lamp you plan on using, the side under the shelf is going to get a lot less light. Probably so much so that you won't be able to keep a lot of photosynthetic corals on that side. But, there are non-photosynthetic corals such as sun corals and certain gorgonians.