-A good way of looking at the fretboard is one that makes sense to you. This is the way I started out as well.
- Em Pent scale: E-G-A-B-D-E-B-D-E-G (in the shape you laid out above in TAB)
- Em scale: this would be your E major scale with the third dropped a half-step. It's a lot less rock/blues.
If you're worried about theory- you can melt your brain here:
http://www.musictheory.halifax.ns.ca...or_scales.html