Subtitle muxing

[Selur]

I am always struggling with automatic mux of subtitles back to result file. How to set up ?

No clue what you are doing. Subtitle muxing works fine here.
-> explain in details what you are trying to do

it is possible to prepend the relative paths for movies in subdirs and save them in same tree structure in target folder instad of only files without dirs ?

Did you look at the settings under Config->Paths?
If you enable "Config->Paths->Adjust->Output path to source path" Hybrid will save the output into the input folder, but if you misconfigure it you might end up overwriting your source file. So make sure you know what you are doing.

Cu Selur