You use RealBand, try this out and see how you go, then you will want to download the above template UserTracks Simple Bar to Bar Matching

Compare these two
This is the drum template flute
https://www.dropbox.com/s/4s3syb5q89pi2gg/_BREATH-Demo-Flute.mp3?dl=0

This is a UserTrack with count to shows where the beats are going, the pink is generated playing the wrong section and over transposing parts, the orange track was manually made, plays the correct beat, plays the correct parts in the sections and plays the set fill on bar 32.
https://www.dropbox.com/s/exrzkdsnrzkqc5s/RealBand-3-4-UserTrack.mp4?dl=0