I imported pair-ends reads (PE300, Illumina HiSeq 4000 PE100, fastq files with quality at 33bp) with the manifest option reporting R1 as Forward and R2 as Reverse reads in 2 separeted column on top of the sample-id column.
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.tsv
--output-path demux-paired-end.qza
--input-format PairedEndFastqManifestPhred33V2
Manifest:
I would not worry about it... it's true that reverse reads typically have lower quality than forward, but this is not a rule
Someone on this forum (can't find the post) recently reported that their sequencing company mislabeled the forward and reverse reads, so it's also possible worth quickly inspecting the reads before importing to see if the orientations are clearly reversed (e.g., if primers are still in the reads or if there are other patterns to search for)