A neat functionality in bash and other common Unix based shells is that you can have variables. So you can do:

(navigate to one directory)

src=$PWD

(navigate to another directory)

dst=$PWD

(navigate wherever you like)

You can now do: ffmpeg -i "$src/scene1.mp4" "$dst/output-scene.mp4"

If you avoid spaces and other special characters in directory and file names, then you can skip the quotes.

This is conveniently not limited to a system wide partitioning scheme.