There is not really a right answer when it comes to choosing which mode of which scale should be played on the chords of a chart. The most fundamental answer is to let your ears be your guide. Yet, some choices may be better than others.
Beyond simply looking at the chords above the staff, it is often useful to acknowledge the melody. Consider the progression in question:
B-9 - Cmaj7(#11) - Fmaj7 - E-9
The first chord could go with B Dorian, or B Aeolian, or maybe B Locrian if you don't take B-9 too strictly. Looking at the Real Book, the first bar contains only an F♯ in the melody, so whatever scale you choose should probably contain an unaltered 5th. The second bar contains a G in the melody, and in the notated chord; this is the 6th of a B-9, so you might consider using B Dorian on the first chord; on the other hand, you might like the sound of a G♭ in B Aeolian moving up to G♮ in the next bar; there really isn't a right answer here.
The second chord could be C Lydian; since the melody in this bar contains a G, you should probably favor this to C Lydian Augmented, which would contain a G♯.
The third bar contains a B in the melody, which is the ♯4 of the Fmaj7 chord. So while you might play F Ionian here if you were only reading the chord names, you should probably consider F Lydian or F Lydian Augmented to acknowledge the melody.
The fourth bar contains an F♯ and a C♯, so you might consider that the piece is temporarily in the key of D, choosing E Dorian for this bar. This acknowledges all of the notes in the melody in this bar, and acknowledges the D that ended the previous bar.
So, there really isn't a right answer to the choices made here, but a good strategy is to look at the melody as a guide. You may also reharmonize the melody; the new chords would then suggest new choices. If there is an underlying principle here, I would say it is that you should consider the options for a particular chord quality, and then look to the melody (before, during, and after the chord) to see what the melody is doing.