How do I connect the two (minor pentatonic mostly), say I'm playing b mixolydian, how would i know which minor pentatonic to go to?
Thank you
If you're in B mixolydian, you're playing in B. If you play the B minor pentatonic over you will hear the clashing note D. Sometimes this note fits in, sometimes it doesn't.

You can't just play C#m pentatonic over B mixolydian. The pentatonic scales aren't shapes that you memorize. They're groups of 5 consonant notes over every octave. There's a "mixolydian pentatonic" scale you could learn, but I don't know it.

I'd say you oughta apply what you've learnt about pentatonics and learn the notes all over the fretboard, not just in the one position. You'll see that it's not a "shape" but a "sound."
Bob -
you can play C#m pentatonic over B, the notes create more suspended feeling than most obvious G#m pentatonic over B
you can play also Bm pentatonic over B mixolydian to create blues feeling
and you can play B dominant pentatonic which is B, C#, D#, F#, A
and yes they are shapes perfect to memorize on guitar fingerboard
Stick with B minor pent but watch for the minor third -'ll want to bluesefy it or simply play the major third, depending on the line.
C# minor pentatonic has the same notes as B mixo, so playing it will result in the same sound. It won't sound more "suspendedl" as suggested above because it is the same notes.

But really TS you are approaching this all wrong. You should

(a) learn your scales all over the fretboard instead of in just one position to allow you to play things like B mixo starting on the 4th fret without calling it "C# minor pentatonic"


(b) give regard to the key that a song is in, rather than the scales you are playing over it. The key will determine what your notes sound like.
And no, Guitar Hero will not help. Even on expert. Really.