After playing enough, you'll eventually be able to instinctively know where a note falls rhythmically in a song based on when it appears on the screen, even if you've never heard the song or played the map before. Of course, this is harder for maps with more complex rhythm patterns (syncopated streams, 1/3, etc), but it's possible.
Once you've played a map and have a general idea where the notes go, the timing should come naturally. Most of the time, I just keep a basic quarter-note beat going in my head (the percussion is often useful as a metronome) and tapping the notes where I know they go in the meter. Only if I can't get a pattern down naturally will I try and link it to an instrument in the song.
As a side note, I always do terribly on auto-pilot. I"ll get like 90% with AP on songs I can 98%+ on no-mod. I don't really know why.