Galaxy Blast gene sequence

Question

[Rob]

Hello friends I had run MaxBin2 from the Metagenomics Analysis in Galaxy. I produced 2 bins. Now, I want to use BLASTn to see if my bins have the a sequence match to one or more of the genes in other fasta file as a reference file. I have so a few questions:

1. Can I run this for my two bins at the same time or I should do it one by one?
2. Which one I should select as "Nucleotide query sequence(s)" and which one as "Subject database/sequences"?

thanks