Hey there @Jane_Lucas!
Okay!
Maybe not - if there are only two files with all the samples in them, that indicates that things are still multiplexed.
Not having a separate barcodes file is fine, we have plenty of options to get around that, but they require that the barcodes are still present in the read itself, rather than in the header. Is it possible the barcode is in both the header and the read? If so, then check out this community tutorial for demultiplexing using q2-cutadapt.
If the barcodes are only in the header, then you will need to find a way to demultiplex these reads prior to importing into QIIME 2, as we have no way to demux reads based on headers. Once demuxed, you could import using the fastq manifest.
Keep us posted! 
