However, I now want to join my forward and reverse sequences together with BBmerge before using QIIME2. I successfully merged each pair into one fastq file, but now I do not know how to import the files.
You can still use the manifest format to import your joined reads, update your first import command above to typeSampleData[JoinedSequencesWithQuality] and you should be good to go.
The manifest file also was changed, for one line per file with direction "forward" for all. I didn't realize I still needed the "direction" column, which threw me off.