I carry them separate only because that is what works for me.

I use my Fatboy daily as my "man purse" so I have a little more room to play with.

In my Fatboy, I have my PSK and a small FAK, in addition to my little red "bag of tricks" (tape, backup matches, twist ties, etc.) for minor emergencies/improvisation.

Having them separate allows me to carry more stuff and be a little more flexible in it's use (for example; I can hand over my FAK to my wife and still have the rest of my gear).

It's fun to play with different configurations of stuff and see how it carries/works/doesn't work depending on real life experience.

My only advice is to stay flexible, play with what works for you, and have a backup for your backup.

One never really solve problems; just trade off consequences.