In a nutshell…
You traditionally animate the part of the character or scene normally, leaving out those body parts or elements you intend to cell swap.
The traditional part of the scene should be behind the cel swap stuff.
Create elements (layers) for those parts you intend to use different variations of for cel swapping which are in front.
Add a master peg to the unit of traditional and cel swapped body parts for characters to move them in unison. You can therefore NOT do hand drawn “camera moves” but rather all movement must take place in a fixed position
(i.e. walking on the spot) and then actually displace the character along the X-axis using the peg for the movement.
If you intend to do drawn camera moves, it will be very tricky to line-up and resize (even skew) the swapped parts to match which is why I recommended not doing it. It can be done but it’s also likely to require a lot of time with the fine adjustments. Do a small test sequence first if you intend to go down this road to get a feel for what’s involved.