First I would like to thank whoever developed this awesome tool that is FFAStrans! and also I'm noob at this, so bare with some basic questions.
Second, I'm trying to create a workflow where the objective is to Add an intro + Main clip with an animated logo and a graphic overlay + 3 outro clips, and export everything to mp4.
I got the workflow working easily, but the problem is that the animated logo overlay (in loop) starts at the very beginning of the intro media and I only want it on the main clip (after the intro clip).
I think you should apply your logo+overlay BEFORE insert your intro.
So apply your different overlays on the main clip ,insert your intro, yours outros and encode. I think no matter the order in the workflow, the important is to have the good order for your output file.
Try it and tell us