Well for me since I work in FLSTUDIO, I just make each sound an individual track running it thru it's own channel on the FX bus.

generally the kick and bass are tracks 1 and 2. Then add your layers from there to build the track.

Generally it is best to group the patterns into sections. Maybe have perc all next to one another, kick drum changes, synths and edits and so on....

Seems to keep the projects well organized while you're working on them.