I'm running a two tier game where my players not only play the rogue trader and his retinue, but also a squad of guardsmen attached to the rogue trader's house Troops aboard his vessel. 

Some Premise before my question:

The Rogue Trader was the captain of an Imperial Navy Vessel bound for the Spinward Front who just got his warrant about ten years ago. as soon as he got his warrant, he was given the ship he was already in command of, and claimed ownership anything and everything onboard his vessel, including the ten thousand Imperial Guardsmen garrisonned on the Defiant when he became a Rogue Trader (this has done nothing to ingratiate himself to the Munitorum, and that's gonna lead to some interesting side adventures) 

now to my question: How would Designing a Regiment of House Troops work? and how would requisitions and starting gear work for House troops, even newly minted ones like these? I would assume that they would have better gear, but requisitions would be harder, as they would have to rely solely on their new benefactor for resupply. what do you guys think?

First, awesome.

Second, resupplying. I expect since the RT only has to keep control over 10k troops, logistically, he's going to be better at it (or his subordinants are) than the Munitorum (heresy, I know). However, fluff-wise, this leads to some issues about the fun parts of Logistics, which is failures or wacky equipment that you weren't supposed to get.

So, maybe the guard is under control of a general, or somesuch, who maintains strict rules about weaponry and stuff (as per normal). i.e. require the guardsmen to keep their Uplifting Primer, can demand their SRK back at any time, etc. That way some of the rules and mechanics of OW make more sense. In addition to this, perhaps the RT is incredibly bad at logistics or doesn't care enough to hire someone who is, so the general needs people to constantly negotiate with other people to get the right stuff to the right places.

Anyway, I think you could fluff it so it works normally. The RT is going to have access to a bunch of fancy crap, but using Acquisition for 10k plasma guns is going to be VERY rough on the profit factor. So, I'd combine them. If the RT PCs want to Acquisition something for their entire IG Regiment, go for it. But, if the OW PCs need to Requisition normal items for their specifics missions, go for it. Basically, use both mechanics normally.