Jd Smith1
Hero
Sounds like a good campaign.We played a very successful inquisition based campaign years back - before any of the official 40k RPGs came out. In that campaign we were agents of the inquisition, rather than full-on inquisitors. That was great fun, and put us in a position where we were more like spies and investigators finding out what was going on before the actual Inquisitor would decide to get involved. We had very little direct authority or power in the eyes of other Imperial organisations like Space Marines or Adeptus Mechanicus. We might bully local authorities somewhat but even that was very difficult and they had limited resources we could call on.
I think the way to approach a campaign like this is that it will be closer to Call of Cthulhu or (unsurprisingly?) WHFRP than it would be to a game of D&D or Traveller.
Obviously that might not work for your group, @Jd Smith1

I plan on the PCs being agents, and low-ranking ones at that. I expect that they will pose as Administarium auditors a great deal, which would give them the authority and rationale to poke around without exciting nearly as much interest as the Inquisition would.
They're not going to be routinely trooping around in carapace armor lugging chain swords; they're not going to arrive on-planet with their own battlecruiser.
They going to show up inquiring about the failure to file full and complete Imperial Form XM-1187b on time. And to inquire why the submitted Imperial Form LB-477c shows a 5% discrepancy for the power generation station on the Isle of Ventura.
While the Imperium leaves most details of planet management to the Lord Governors, there is no reason to expect that they absolve those planetary administrations from reporting data.
Again, as the canon provided by Dan Abnett, First of His Name and Protector of the Lore, has shown us, subtlety is not a unapproved tactic for the Inquisition.