Given that you're not experienced with it, you're bound to make the occasional mistake. As such, I'd go with the fittings that are most easily redoable while also ameliorating your feeling that they might leak.

PEX has a minimum bend radius before it kinks. It's possible that you might get into a situation where you'd have to bend it more tightly than its rated for. In that situation, you'd use an elbow fitting.

Keep in mind that with a manifold system, infrequently used faucets will create a column of stagnant water, which can lead to certain bacteria being able to grow more readily (think Legionnaire's Disease). For those outlets, I'd try to avoid a home run.

If you're going to run a whole new system and not just copy what the copper is already doing, you'll likely have to cut new holes in joists and such. Make sure you look up what the code is on cutting holes in load-bearing members. There's a reason that carpenters refer to plumbers as being worse than termites.

They make a tool for cutting flexible plastic tubing. It kind of looks like pruning shears. I'd definitely get one of those rather than trying to cut the PEX with a utility knife like LBT showed in his video.

Assuming you want to remove the old copper piping, I'd still suggest a tubing cutter. It's remarkable how well they work, and it's very tidy.

Oh, and make sure you have a good number of towels and buckets to catch water that will leak out of the existing system as you disconnect it.