Skyline allows you to add multiple FASTA files to a background proteome.
If you already have a background proteome (.protdb) file, you can go to:
Settings > Peptide Settings > Digestion
and choose "Edit Current" from the "Background proteome" dropdown.
Then you can add another FASTA file.

By the way, if you are ever faced with a situation where you are only allowed to use one FASTA file, you can always use a text editor such as Notepad to create a single file which has the contents of both of the FASTA files.
-- Nick