The below is a work in progress. We are actively working on this area of the ARDUX QMK code.
You need to set ARDUX_REMIX=yes at build time (see DEVELOPMENT.md for additional detail) so your remixes and adjustments will be included in the build.
To adjust any/all ARDUX non-combo keys you can create a file at users/ardux/layout/remixes/remix_layers.h with the contents of the adjustments you'd like. You'll want to define the entire layer like we do in users/ardux/layout/layers.h for the override to work.