Hi @Danilo_Reis,
Welcome in the forum!
To answer straight to your question, if you prepare a manifest file for the importing step, you don't need to move all files in the same folder, as long as you specify the path for each file correctly.
However, there are few things to note. I don't think qiime2 is able to work with 'bz2' files, hence you may have to decompress (then recompress with gzip if you want to save space, you can import as 'fastq.gz' files).
On the files you need, you probably want to import R1.fastq.gz and R2.fastq.gz, as paired files, as described in the Importing data — QIIME 2 2020.11.1 documentation (Casava 1.8 paired-end demultiplexed fastq ). What you need to understand is if these sequences have been preprocessed somehow or are raw (eg containing sequencing adapters and low quality tails), to see from which point of the analysis process you need to start.
Hope it helps
Cheers