Modal music has more to do with the harmony then the linear improvisation, for instance if you write a song based in C major, C is going to be your tonic chord that everything gravitates toward, and yes your right, certian notes are going to sound better (or stronger) then others, music is a hierachy, not a democracy.
Now try writing a song where the seventh chord of C major is the tonic (B-7b5), now you have modal music. Most modal songs (or jams) are only constructed out of 1 or 2 chords, because once you start to bring in other chords from the scale you start gravitating towards the the tonic of the major or relative minor.
Like anything, the best way to grasp modality is to listen to recordings of it, check out So What by Miles Davis, one of the founders of modal improvisation.