Samples are inserted on a per-song basis meaning whatever you have inserted doesn't affect other tracks. In fact, AMK will omit any unused sample which isn't marked in a sample group to be mandatory. So just because you didn't include, say, sample 11 (bongo drums) in a track, it doesn't mean that none of the music will not insert the bongo drums.
When samples are ommitted, it's because the music in question use large enough samples and/or a large enough echo delay that there is no way to properly fit all vanilla samples into ARAM with the current music. Typically, it's done by ommitting samples which are used in local tracks only i.e. neither in global tracks nor sound effects: 0D (slap bass)*, 0F (bass drum) and 14 (distorted guitar). Some more are only used in global tracks and and sound effects can also be sometimes ommited should you run out of ARAM. Here is a small list of these samples:
- 05 (bass): Starman
- 07 (oud/guitar): Course Clear
- 09 (steel drum): Bonus End
- 0A (piano): Player Down
- 0C (electric piano): Game over
- 10 (bongo drums): P-Switch
- 12 (orchestra hit): Yoshi, Bonus Clear
- 13 (thunder): Thunders but also Blarggs
Some are bigger than others and thanks to their easy workaround i.e. unlikely use in context, it's easy to omit e.g. 09 which is one of the larger samples and used in the most rare local track but also common targets are Orchestra Hit (you can easily filter Yoshi, for that matter, not to mention many don't use him at all or with a counter break together) and Thunder (only used by one enemy as well as a rarely used effect).
*Though both AMK sample groups mark it to be always included. Can anyone give me a counter example for that i.e. any local track which uses it?