Question about HUMANN3

Metaphlan supports great help for my soil metagenome data to classify the taxonomy.
But I got stuck when using HUMANN3 to generate the function information from the metagenome.

First of all, how to get the pair-end data into the input file of HUMANN3? Because HUMANN3 allows only one file as input. Did I miss something?
Or do I need to merge the pair-end data using software i.e., FLASh? This is what I have done.
the command I used is below,
humann3 -i L288/L1EEK060288_E31_S183_L002.merge.fq.gz -o new_L288_results --nucleotide-database /public1/downloads/db_humann/chocophlan/ --protein-database /public1/downloads/db_humann/uniref90_diamond/
Or do I need to cat the pair-end sequence file into one file? It implies that the overlap information of pair-end data was ignored and pair-end data was juset treat them as individual reads file.

Besides, I didn’t find a tutorial of HUMANN3, e.g. extraction kegg or other information from result or the choice of “usearch or bowtie or diamond”. Could you supply some resource?