in order to align genome multi-fasta files, do you ignore the chromosome sections?
If the fasta really are chromosomes, there will be one per chomosome. Check this in case the multi-fasta you have is an incomplete sequencing of an organism. If incomplete there will be many more fasta. There is a bioinformatics site on Stackexchange now at https://bioinformatics.stackexchange.com .You would get better answers there.