Hello, so the way outgroups work is to add it/them among your inputs and the re-root the resulting phylogeny w.r.t. it/them.
In your case, if I have understood correctly, you have a genome from archaebacteria that you want to use as an outgroup, so after PhyloPhlAn builds the phylogeny you should open it with a software like Archaeopteryx and set the root of the phylogeny in the branch where the outgroup genome(s) is placed.
As far as I know, there is no way to tell FastTree to use a specific genome(s) as outgroup.
Instead, if you use RAxML (https://cme.h-its.org/exelixis/resource/download/NewManual.pdf) or IQ-TREE (http://www.iqtree.org/doc/iqtree-doc.pdf) there are params to set an outgroup, and if you want to exploit this option you can edit the configuration file and add to it the specific option so PhyloPhlAn can run it.
I hope this helps.
Many thanks,
Francesco