Hi,
Did you try the following command?
qiime tools import
--input-path sequences.fna
--output-path sequences.qza
--type 'FeatureData[Sequence]'
If you have separate fasta file and quality file you can convert them to fastq file first using QIIME1 script
convert_fastaqual_fastq.py -f seqs.fna -q seqs.qual -o fastq_files/
If you have different naming of the files than the standard format, check out #“Fastq manifest”# formats Importing data — QIIME 2 2017.12.0 documentation
kind regards,
Dorothy