Technically they're two different institutions, the Skitarii essentially being the military arm of the Cult Mechanicus but not actually a part of it if I remember correctly, although it's a very sketchy excuse for charging you for two Codexes instead of one. Most people will bring Adeptus Mechanicus armies, which are a combination of Cult Mechanicus, Skitarii and Imperial Knights, some houses of which are sworn to Mars. Basically, in fluff, the Skitarii and the Cult Mechanicus and the Mecanicus-aligned Knights are all allies, not one army, but for some reason that's also been put into the tabletop in a somewhat arbitrary fashion.A bit off topic but
What's the difference between skitarii and cult mechanicus? Like why are they different and have two different codex's?
I am quite interested in starting a mechanicus force but I'm a little confused.