So, I think it's best to understand the purpose of a safe room, which I think will help answer your questions.
A safe room is a used so that your new kitten will not feel overwhelmed by all the new people, all the new smells, being lost and not knowing where his litterbox and food and water is, and allows him to slowly acclimate to his new digs at "his pace". Some kittens see a new home and immediately want to explore. But many just want a place to hide and deal with their fear, and sorrow, and loss. A safe room is also of greater importance if there are other animals in the house that may require a slower, more careful introduction (which sounds like it may not be the case for you?) and/or a quarantine.
Many people use a bathroom as a saferoom. It isn't ideal because it's not a very pleasant place for a cat, and there isn't much to interact with or explore once they get the urge to do so, and most importantly there often is no place for a scared cat to hide, but it might be preferable to putting the kitten in a huge open space where he is overwhelmed. To me, I think your best bet would be to use one of the upstairs rooms, bedroom or office rooms. What you need in a saferoom is food, water, litterbox, toys, and a place for the kitten to hide. Giving a kitten a place to hide and allowing him to do so if he needs to gives him a sense of safety. How long to keep them in the saferoom? For me the criteria was simple: as soon as the cat shows interest in what is behind the closed door, then he is allowed out to explore that space.
Definitely don't move litterboxes!! Once you have a cat that gets used to peeing and/or pooing outside the litterbox, that is a huge problem. A lot of cats are re-homed because of that, and it can be challenging to re-train them to use a litterbox. So you don't want to go there. So my suggestion is have at least one box on each level (maybe more depending on the size of the place, and whether or not the box may be closed off from him from time to time). Use very large, open boxes ideally. And start with the litter he is used to from his breeder, then change over to one you prefer if you like. And definitely you want to strive for consistency. Cats are creatures of habit. Litterboxes are always kept clean and in the same location and with the same litter (once you've established the one you want to use), and always accessible.
Cats love vertical space, especially bengals. The desirability of a spot to sleep in is often defined by how high it is off the ground (and it's proximity to his "people" and things like windows or other interesting things to watch). I have one tree and many high perches in each of the rooms that I spend much time, and they are always in one tree or another pretty much. Criteria for selecting a tree: It's height (taller is better), the stability of it (cats hate climbing rickety things that can't support their weight), and the material (sisel is good, as are well carpeted surfaces). Also when you buying a tree, fix your eyes on the top perch in the tree (which will be where your cat spends all his time
), and see if you can trace a way down from there for your cat without what I call a "crash landing" (where they are compelled to basically plummet all the way back down to the floor in one jump). Some trees are incredibly poorly designed in that aspect, and to make them useful you need to put other structures next to them so the cat can climb down reasonably.