Hi again,
I am back with an update. I ran both suggestions so
a) DNA and RNA together at lowered qual setting (ie. --min_per_read_length_fraction 0.68)
b) DNA separate, again using 0.68
c) RNA separate at default settings (0.75)
checking for possible effects it was plotted in a MDS plot.
I'll just show the RNA samples here (they were rarefied to smallest sample size and this was the same in a), b), c). Nothing else was done).
This is from option a)


this is from option c)


To us it looks the same, and the DNA distributes differently from the RNA, but between QIIME-runs it seems like the same.
in the end it was decided to go with option a), as it was very few reads in difference between RNA at 0.68 and 0.75 (the fear could be to open up for alot of "bad" reads), and that it might be easier to justify with a uniform strategy. But again, now we tested it.
If you have any additional comments they're welcome :)
Thank you for all the help.
Cheers,
Sachia