Haha, really no magic, nor rocket science here.
Starting work with Chipper I've tuned two basic instruments (using Atari 8-bit music program Chaos Music Composer).
Feedback and Timer gauges are revelant below:
1) Pure sound:
2) Bass sound:
Other sound (ie. for percussion) may come from another Feedback settings.
All the rest of "magic" is to manipulate all the rest gauges (ie. Shifter, Behaviour and Volume) to make instruments sound different.
Regarding my workflow there isn't one recipe. Sometimes I start simply with Chipper, sometimes I use some RMT (Raster Musoc Tracker) tune (or at least its matrix) and sometimes the source comes from MOD file, so there isn't one way I work with Chipper.