Yes, you're correct - only one SSH user per domain. Users are the same whether they're FTP or FTP with SSH, only one for a domain and any others you create will have their own non-web acceccable space enless they're the owner of a domian. So yeah, you have to log in with the user for that domain if that's where you want the files.
As far as using FFMPEG you'll have to point what ever you're doing to the appropiate place. You'll want to update your path. The OS isn't magicailly going to know that you've got this program - you'll have to point it there.
log into SSH
type "nano -w .bashrc" and press enter
add this on it's own line after anything that's already there:
press ctrl-o to save, press enter to accecpt the same file name, and press ctrl-x to exit. this should get it working for a website script. Add the same line to .bash_profile for use from shell. It may be that you need to add in your lib directory if things arnt working yet, just edit the above file again and add in lib:
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