I was thinking of prewiring and having everything ready as they build out the basement
1. In-walls vs freestanding speakers?
2. If freestanding, bookshelf vs towers? I would do towers if you are going to use freestanding speakers for the surrounds. Atmos would be in-ceiling. Surrounds would usually be closer to ear level, usually not in-ceiling. But if you don't want to do freestanding towers for surrounds, in-ceiling surrounds would have to do.
3. 5.2.4 is good IMO
4. Talk to your dealer to see if they can offer you a good deal.
