[HELP] managing audio & subtitle from many videos

[Selur]

I have 1 line in the audio queue dealing with the 1st video

Yes, if you want to configure something for the 2nd title you need to change the source in in the Audio-tab,...

the 1st episode has only the aac audio track without subtitle

Naturally, since you didn't tell Hybrid to automatically handle the subtitles (Config->Automation->Passthrough streams->Subtitle) you only told it what to do when you:
a. select all subtitles in the man and add/extract them
b. passthrough or add auto add all audio titles
-> so you configured stuff you didn't use, you might want to actually read the tool-tips Hybrid provides for options to understand what they do.

the others have no audio & no subtitle

Naturally, since you told Hybrid you'll use custom settings but only provides them for the first source.

what I did in config -> automation don't seem to be corrrect

What you thought the settings you enabled do doesn't seem to be correct, I agree.

Cu Selur