For example, looking at BB3 in C Major on page 90 in the manual "anchored"/rooted on the 5th string.
To play A minor you could start on the 6th string A, 5th fret, which along with G at the 3rd fret would be starting BB1+1.
So in C Major I would envision BB3 stating on C on string 5 and in A minor I would envision BB1+1 and start on A on string 6.
Even though connected you have all the same notes either way: G A C D E G A C
If you played BB1+1 in A minor from it's b3 which is C you'd be playing BB3 in C Major.
Thinking in terms of playing a relative scale over a key rather than in terms of the key's own scale would be too confusing for me.
But some people do it.