Hi @slh277!
There are a few options here --- if the primers you need to remove are on the 5' end (and of a fixed length), you can use the --p-trim-left/--p-trim-left-f/--p-trim-left-r parameter(s) to specify a suitable trim length. If you need something with a bit more control, you can check out the q2-cutadapt plugin tutorial, in particular, the qiime cutadapt trim-paired method.
As far as your feature counts in Q2 vs Q1, those could certainly be impacted by adapter sequence, as well as truncation parameters, but DADA2 is a different method than OTU clustering altogether, so you can expect to see some differences. For more info on that, check out this post from @ebolyen and this post from @jairideout (these posts both have some general descriptions about DADA2 and ASV methods, but they do go into some other details that probably aren't relevant to you here). Finally, the DADA2 documentation and tutorials are an excellent resource, so please be sure to spend some time catching up there: DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
Keep us posted with any more questions, thanks! 