Watch the Shackman online guitar lesson by Chris Buono from Funk Fission
Time to drop the pick and discover the awesome possibilities of your pick hand. Some advantages to a pick hand freed from the confines of holding a pick are the overall tonal changes (skin and bones sound considerably different than the pick on the lower notes) and the added appendages available for more complex playing (your thumb and first finger (P1) are now part of your arsenal). Notice the P2 pops are now P1 pops and the previously downstroke picked muted sixth string events are now thumb mutes.
The real deal here is the "technique motif" concept talked about starting at 2:36. The idea is the pick hand performs the same basic order of attacks on the strings allowing you to focus on variations in pitch and percussive options made by the fret hand. From there, you can go off on tangents for even more variations. The benefit to this approach is it gives you a firm foundation in one hand while the other starts to explore new ideas—less confusion. Then, when you’re ready, start to vary the pick hand techniques with techniques like the first finger/all four finger whips I lay down at the end of this segment.
If you look closely at the riff I play at the end starting at 3:13 you’ll notice my thumb gets a workout between the thumb slaps, thumb mutes, and the reverse rake at the tail end of the 3rd beat in bar 3. When not doing straight up thumb mutes, my thumb in downstroking notes in a similar fashion albeit with different dynamics as evidenced by accent marks or lack thereof.