In this example, Einojuhani Rautavaara sometimes uses flat and sometimes uses sharp in some chords.
Once it's atonal music, what're the rules for sharps and flats?
Fair question. Think about these things:
1.) Context (lots of sharps / flats already? Which would simplify the music?)
2.) The direction (sharps = up / flats = down)
3.) The instrument (strings more comfortable reading sharps / winds more comfortable with flats)
4.) Writing intervals the way they sound (does that really need to be "C-D#" or would "C-Eb" make more sense?)
5.) Voice-leading (this is part of "context" from above - what makes the most sense voice-leading wise? Atonality and functional harmony can coexist; just because your chords have functional voice-leading does not mean that they can't exist within an atonal framework.)
Make the decisions that make the most sense. The more you can simplify the music, the better.