Under the student right hand exercises section on the alternative picking exercise pdf, can some explain what the black squares above the 6th string and 5th string and the #2 & #3 (are those finger numbers?) are in the first neck diagram example? Thanks so much!

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Those are marking "string sets" or string pairs.

So at the top you have 6,5 then 4,3, then 2,1 and you see the "down" "up" pick markings at the bottom.

So you pick down on 6, up on 5, down on 4, up on 3, down on 2, up on 1.

Great, thank you, that makes sense! Do I need to do anything with the 2 & 3 string circles?

Those are telling you which fingers to use on those strings.

Pebber has some videos, titled something like "How to take the online lessons," where he explains a lot of these concepts.

Thanks, I will look for that video! I assumed that, but it has the up/down indicator on the bottom of the 6th & 5th string but nothing on the 3rd string that has the 3 tab so that is what I didn't understand.

That's because each image as you go left to right is only a portion of the total picture.

It's telling you:

fret the 5th string 2nd fret with your middle finger, 3rd string 2nd fret with your ring finger
pick down on the 6th string, up on the 5th string
pick down on the 4th string, up on the 3rd string
pick down on the 2nd string, up on the 1st string

Thanks Farelli! It hit me this weekend, seems so obvious now