Originally Posted by: jedftIn some lessons they are using a higher note as the root (I) and lower as the IV and V. In others, the lower note is the I and the IV and V are higher. How do you know which way to play it?[/quote]
It depends entirely on which sound you want.

Since you can do it either way, you should be aware of either way, practice both ways and be able to do both ways. That way you can try each as the situation comes up and see which sounds better to you at the time.
[QUOTE=jedft]
If someone says 12 Bar Blues in D#, my instinct is to start at the 11th fret on the 6th string and use an E shaped chord, then going to an A shaped chord at the11th fret on the 5th for IV etc. But in the D# lesson she starts at the D# on the 6th fret of the 5th string, then uses the E string for the IV and V. So how do you know when to start higher and when to start lower?

Again, it depends entirely upon the sound you desire. They do sound a bit differently. And also different positions will allow you to play certain things that are easier in that position than others.

For example, if you want to put some pentatonic blues licks in between your chords, then you might prefer one position over another in order to get from the chords to one pentatonic box pattern rather than another.