Learn them starting on every note in the scale on each string. That gives you every single position and all those sounds will “work” over an E major sound. When you start on the 2nd, 3rd, 4th, etc scale degree, it can be called a “mode” but just think of it as “E major scale starting on F# (or the 2nd) “ There are only 2 places to start E major on the root on the E string (0 and 12th fret). To learn the different positions, start on each note of the scale on that same string.

For starting notes on the E string with fret numbers: E: 0 F# (dorian): 2 G# (phrygian): 4 A (lydian): 5 B (mixolydian): 7 C# (aeolian, natural minor): 9 D# (locrian): 11

These sounds all fit over E major if that is the tonality in the bass/chord progression. They also fit over a multitude of other sounds.

The mode names are related to the starting pitch, so “A Lydian” just means playing the E major scale starting on A.