Hi @arwqiime,
If you are planning on using dada2 in qiime2 it is better to import your reads unjoined as dada2 performs denoising on individual reads and then merges them. See this thread where a similar question was discussed.
If your plan is to use another method such as vsearch, I think this tutorial can help with your importing questions. Specific to your question, see the
Importing pre-joined reads
section.
Hope that helps!