Hey, in the bastardkb docs, there is a tray holder for the nano/pro micro that looks to fit inside your build, also works on my Scylla. It's its own repo. I think you can slip the battery between the pins.
Then check if your are rol2col or col2row, there is explainer inside the zmk docs.
Next, find the pins, n!n pinout, and make sure your overlay and dtsii? File has the right order of matrix,. eg the 0,0 0,1... 0,5 and that it matches with how you wired your board. And the right row2col setting.
Zmk docs also has a nice explainer for he matrix stuff.