Layer stems or place them back to back?
Layer Together plays the stems you pick at the same time, as one sound. Place Back-to-Back puts them one after another. Layer for a blend, like drums with bass. Go back to back when each part should be its own section. Then choose where the result goes.
You make this choice after separating stems. It doesn’t change separation quality, so listen to each stem first.
For S9 Sampler 0.1.6 (paid beta). More help inside the app: Help & Shortcuts → Separate stems.

Step by step
Listen to each stem
Play each stem and the original. Keep only the parts you need.
Together or in a row
Choose Layer Together for one combined sound, or Place Back-to-Back for a sequence. Drag the numbered items to reorder them.
Choose where it goes
For a whole sample: Replace Sample, Add After Sample or Insert After Chop. Selected Chops have their own replace, insert-after-each and add-at-end choices.
Apply and check
Listen to the result and look at the new Chops. Back-to-back Chop stems get their own cuts, and one Undo restores the whole batch.
Good to know
Keep the original
Adding or inserting keeps your original audio. Replacing is always an explicit choice.
Layout won’t clean a stem
Rearranging doesn’t remove bleed. If a stem isn’t clean enough, try a higher quality setting or another source.
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