Hi @cecibe,
Where your barcodes are is all going to depend on how you constructed your sequencing library. Your 2 fastqs are probably the forward/reverse reads, and the barcodes may be in-line in the sequences or in the header lines — it is impossible to know without getting that information from the source (or you could check the first N nucleotides on each sequence to see if these match the barcodes in your sample metadata file). Check with the sequencing center, lab, or whoever did the library prep/sequencing, that's the surest way to know.
Once you figure out where the barcodes are, I can point you in the direction of the correct method for importing/demultiplexing.
Good luck!