This topic might be useful for you.
If primers are contained in the sequences, you may be able to use q2-cutadapt to separate out different marker regions prior to dada2, adding part of the primer sequences to the barcode sequence listed in your mapping file, as described in that topic. Note that you will want to trim out primers before running dada2, anyway, so this may be the way to go.
Alternatively, use exclude-seqs after dada2. There is no need to use primer sequences (though you could if primers are still in your samples), you would just use two different reference databases for filtering.
I hope that helps!