These won't be comparable with what you get out of :qiime2:. For marker genes, i typically assume that what's in the repositories is unprocessed because that's the policy for most repositories. So, I would recommend processing them the exact same way. I would also verify your primers and the primers for the region you're downloading. Microbiome data is sensitive to technical effects, and so its important to make sure things line up correctly.
You also need to be aware that the length of your reads will dictate how you can combine sequences, so if you can't join, i would trim your reads to match theirs.
You want to use the q2-quality-filtering plugin. i recommend default settings, becuase those have been optimized for deblur. The alternative methods of read joining tutorial goes through one workflow.
Im gonna refer you to a couple of threads on that...