SVL, what I find works for me is knowing the sonic difference between a tone (2-fret jump) and semi tone (1-fret jump). For example, in the case you mention some songs call for a major scale solo and some a minor solo and some progressions will allow you to use either/both depending on the underlying chord. As you correctly state the shapes/patterns are the same (pentatonic) but are 4 frets apart. If you start with say a root note of C on the 8th fret E string, you could not slide that note back a semi tone (1 fret) to the B note and have it sound good over a standard Blues in C type progression. However over a major type progression C-AM-F-G that interval will work ok.

So what I'm trying to get at is if in your head you can hear that semi-tone interval before you play it, you can kinda predict whether it will work and that defines what scale you can jam in over the progression. Over time it kinda becomes intuitive and you'll find yourself hitting bum notes less and less. What it boils down to is if you know what a full tone interval and semi tone interval sound like from your current note, and you know the major/minor patterns on the fret board, it becomes very easy to fall into the 'correct' scale for the chords you're playing over.

I'm not much of a theory guy but that kinda works for me.....