You probably want a 3" seat cushion, and you need to decide on welting...typically you'd want it but it can be matching or contrasting to the cushion.

On mine, I had the carpenter build a frame around the seat and cut me some plywood which I upholstered. I stuck it to the back of the seat with velcro. I screwed up though and should've had the frame accommodate the cushion better so the back pads would've been higher...for looks...it's plenty comfortable as is. My bottom cushions are loose.

But there are other ways of doing it too.

If the nook is completed (including stain or paint) you should select an upholsterer who will come to your house and give you his or her opinions and options on the cushion construction. A setup like Annie's is typical, nice looking, and comfortable. You could also have the cushions upholstered to the bottom and top benches, with the fabric stapled over the fill and staples hidden by welting, or,you could have both cushions loose and not attached, with the back cushion's bottom edge resting on the seat cushion, and the top of the back cushion attached to the frame by Velcro or snaps. Alternatively, the back cushion could be made in a wedge shape that narrows at the top, which would keep it in contact with the banquette itself. I have also seen the back cushions suspended from decorative straps over the back of the frame, where they hang down but do not touch the seat cushion. There are many cushion arrangements and the upholsterer/ fabricator will have either pictures or drawings to show you so you can choose the one you like best and that suits your space and fabric best.

I would get in touch with nanny2a, a frequent poster, who has an etsy shop doing exactly this.

Here is a link that might be useful: Etsy shop