There is a zmk pull request open that adds split encoder support. If you use that to build your firmware if should work.
To be honest I have not tried it with this board so technically one scrollwheel is not working right now. Though I'll change that soon. I used a fork that supports split encoder with zmk on my sofle and it worked, so you could use this config for some inspiration (here: https://github.com/dnlbauer/sofle-zmk-config).
No, you solder it in the same way for both sides.
The "flipping" is handled mostly internally. For The right hand side, the firmware just maps the rows and columns differently than for the left hand side. For pins where this is not possible (Vcc, Gnd,..), there are jumpers on the other side that need to be soldered.