I think when you buy them from the Mechanicus you can choose what company they are assigned to. If you want to use them you load them onto ships like marines, but they take up 10x the ship capacity of a tactical marine. Then, to use them go back onto the company screen where you load and unload troops and unload them on the planet you want to use them on. Then once all the troops and vehicles are unloaded from your fleet (it takes a while to click through everything) go the next turn and any enemies on the planet will attack your land army. If there are fortifications your troops will start behind them which seems to be a big help. Once the inquisition branded my chapter heretics and millions of imperial guard attacked me at once and the fortifications lasted several turns.
Some things I've noticed:
The ambush chapter trait seems to make a good bit of difference at the start of a combat so I've been taking it as a trait. I also choose bolter drills because there are many and various kinds of bolter in a chapter. It also makes vehicle mounted bolters better. The third choice is harder, I haven't taken slow and purposeful yet but I think my next chapter will be that. Crafters seems to start you off with more sets of corvid armor; maybe more terminators too but I didn't count either. Melee enthusiast could be useful as it might save you some casualties depending how strong it is.
I think in the first chapter I created I loaded force weapons onto Dreadnaughts and they used them, but the close combat weapons seemed to work better.