IMHO and unprofessional, nonaudiofile, nontonenazi ears,
I'm pretty sure they both have different freq centers, but haven't read the detailed specs of each to know exactly.
The 2band, being boost only, seems to push their respective freq harder than when you boost treble or bass on the 3band. That is, to me, when I push treble or bass on the 3band, it's more subtle. When I push treble or bass on the 2band, I hear RIGHT AWAY that I'm pushing either frequency. Especially when you dime either knob.
That's what I'm hearing initially, live via my rig (GK700RBII and 2 GK NEO 112's) or recorded (DI from my head to Audacity on my PC).
Like many say, the 2band seems 'warmer'. I concur and in my unprofessional opinion believe it comes from what freq the Bass is being boosted. When I start to dial in the Bass freq, it's immediately noticeable and 'fat', 'thick', 'warm', 'full', immediately come to mind.
Yup, the 2EQ is definitely fatter. Probably because the bass knob boosts a wider range of freqs which includes mids. I also noticed that the 2 EQ is the way to go if you DON'T want to draw attention to the bass. It sits better (for a Stingray) IMO. The 3 EQ can put you in front at the twist of a knob which may be something some players don't want.