I'm building this storage bench. Have many ideas how to attach the seat and back to the sides and need opinions what is best. I have a domino jointer, kreg jig, cleats, and guess I could also make a template to cut a mortise into the sides. I'm thinking dominos & cleats right now but if you think something is better please comment. - Thanks

"I could also make a template to cut a mortise into the sides"

If you decide to use loose tenons (I'd), you can refer to the manual and do it as a Carcase Butt Joint. Pay attention to this tip, which is applicable to your case:



There's no need to make any template unless a router rather than the DF500 is intended to be used for this project.

For structural strength and rigidity, the seat and bottom are also joined to the back with dominoes (do plan for wood movement).

P.S. Cut all the joints before shaping the sides.

This diagram would give you a general idea of the suggested domino placements:



I'd also treat the joinery for the dividers and the seat/bottom as  a carcase butt joint, and use the same procedures as laid out in the manual to mill the mortises (but this time, the second tip may apply, if it's 20mm thick or less, or roughly center the mortises). Needless to say, I'd also use loose tenons for all the drawers.

This design so much reminded me of a church pew, that I wondered how those were built.  They tend to get heavy (if not respectful) use and I never came across a rickety one.

Google yielded a trove of information.

https://www.google.com/search?client=firefox-b-1-m&q=church+pew+plans&tbm=isch&sa=X&ved=2ahUKEwiVrMPQ8ZL_AhV0j4kEHSsiCboQ0pQJegQIERAB&biw=1128&bih=718&dpr=2


This company brags about their premium construction.

https://www.churchinteriors.com/pews/

As they say "When you are a hammer, everything looks like a nail". So as a strong fan of the DF500, I would Domino every joint on it.
Yes, taking wood movement into account is important. This would really only apply to the back panel in this case. The sides and the seat go in the same direction.
Are the back of the case and the seat back itself, separate pieces? It's not apparent from that pic.
I would assume so, but it's not a given. You also can't tell if there is any tilt to the upper back.