They probably don't make the car from scratch every season. Pen and paper is perfectly fine for small tweaks and conceptual ideas for very specific parts
Since he came from that era where ground effects played a role in F1 he probably focused on the bottom of the car this year (floor) hence they had less issues with bouncing than other teams.
You will notice he attends most races - he sits on the pitwall.
This has been the way it goes for a long time now. The engineering teams that work on f1 cars are huge (though less so now with the cost caps that came in to effect this season) so no one knows every aspect of the car in full detail. Same as with any large engineering project really.
What someone like Newey brings to the team is working out how the whole thing fits together, identifying the most productive areas of the car to work on (to find more speed) and troubleshooting issues with the car that come up through the season.
Add new tyre compounds to the mix as well.
Merc is not so dominant this years compared to last year because they got it wrong for their 2022 car while Red Bull and Ferrari was out of the gate competitive.