sorry i havn't been around for a bit, anyway here's an answer of sorts..
BTW i noticed you calling me Chi, finally someone who knows what i mean by ki!
yeah, you're right about the scale shapes being shifted, it's just a big fretboard size template which contains all modes linked up, which you can shift around,
and there's other templates you can use instead, like the one which contains harmonic minor, or the pentatonic one(the pentatonic template has 5 modes of it's own because any (pure)pentatonic scale only has 5 notes)
(i referred to those as 'families in the tut)
the chords underneath basically want to be made out of the same notes you are using to solo with
if i was playing chords in B minor(relative lydian is G) that revolve around the B and i played a solo in G lydian, i'd sound like i was playing in B minor, but i'd just be using shapes that i know through G lydian(this can open up your playing too by forcing yourself to use different shape ideas for the same scale)
however if my chords changed and revolved around the G(still only making chords from the notes in Bminor or G lydian)
the solo wouldn't sound minor anymore but lydian
the chords will sound more G lydian if the 'lydian' notes are accentuated
ie. the root because it's our link to G, and the Augmented 4th because it's the note that makes it different from another commonly known scale(in this case G major)
chords accentuating these will sound very lydian
so playing G lydian or Bminor over a B simply sounds like Bminor
but playing G lydian or Bminor over a G will sound lydian
if i played B lydian over a B it would sound lydian too
if you make a backing track that only uses B you could play in Bmajor, switch to Blydian to start giving a modal flavour, switch to B harmonic minor for a buildup
then into B mixolydian for some jazz etc... it can all sound good and like the modes they are because it's always a B scale over a B
if i played in B minor and then switched to a RELATIVE mode like Glydian i'd still be playing in Bminor
if my backing track incorporated a B(root) and a maj2 (C#) and even a Min3 (D)
to solo i could play modes which contain a maj2 and min3
(aeolian,Dorian,harmonic minor...etc)
so the solo could switch at anytime between Bminor, B harmonic minor or Bdorian and sound good(and the modes would sound like the modes they are)
does that make sense?