Hi @AttilaTheBun,
Yes, yes they are 
!
With the multiplexed file, it depends on how it's set up. EMP is not the only way to go. I would look at importing your multiplexed file and then see what you can do with q2-cutadpt. If q2-cutadapt doesns't suit your needs, you could go with cutadapt (or even your in house script) and work with the manifest format.
Best,
Justine