Use the hotkey to toggle always on top if it's hiding the main window: Ctrl-Shit-T
In general it's rare that it is useful unless you're doing very fancy layouts for mouse focus efficiency. You haven't replied to my question above (What did not work with the automatic layout...).
If you can ever reproduce "X didn't always work" please come to discord or open a github issue as I fix all reported bugs rather quickly but I can't fix things that never happen to me and aren't reported.
About MAMA did you follow the steps at https://github.com/mooreatv/MAMA-mul...EADME.md#setup
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