Well, as I mentioned before I got the raw R1 and R2 data and the metadata. The sequencing comany provided a software that takes these 3 files and separates the data into R1 and R2 for each sample,(these are without barcodes, but with the primers,) named like this: sample1_S29_L002_R1_001 and sample1_S29_L002_R2_001, but it also produced two index files. So by the time i thought my sequences could be imported with the casava1.8 process but the software used to separate the samples implies that if you dont want to use these files separated, you can just use the raw data with the index files and do the method you used in your post.
I think I´m overthinking everything and just getting everything more complicated hahaha.