Required Apps (both from BigBoss through the source):
Run Installer, install Categories, and Poof.
Run Categories, create new folder(s) as described therein.
Upon updating any categorized apps though Installer, run Poof and immediately exit the program, which will refresh the updated apps location, no further action needed.
Furthermore, using BossPrefs, you can assign apps to its own dock, by tapping 'More', and tapping 'Dock Icons': Tap 'Add', and then tap the apps to dock in BossPrefs.
Then run Poof, tap those same apps to hide, and they will only be displayed at the bottom of the BossPrefs scrollable dock.