tl,dr; Organizing a Table of Organization and Equipment/heirarchy for a shipborne team sanctioned by the Inquisition but including Astartes elements. Help and comments welcome.
So, I'm going to be starting a WH40kRP game with my local gaming group, and it's kind of Rogue Trader but mostly not. The group is mostly associated with high level groups, a la Throne Agents, but it's a shipborne team, complete with military support. It's operating on three tiers- the strategic tier, using Rogue Trader/SoI stuff, the high-level character tier, using established characters in the Black Crusade rules-set, because it's tighter than RT and uses Influence, the same way Ascension does, and the grunt-tier, using On War because grunts, and I want the chance to practice running On War. Most of this is just rambling background for context.
There are two primary factions to this group as it assembles, as opposed to the more-or-less single faction you see in most RT games. Two of the characters are associated with a Recongregationist Inquisitor (whether she identifies herself as such or not is beside the point) trying to institute reforms in the Imperial structure. Another is a Dark Angels Interrogator Chaplain. Part of the aforementioned establishment of the characters includes accidental association between the more secretive portions of the DA and these characters (and their backers).
What comes from this is a single light Astartes ship, probably a patrol vessel with a squad or half squad of DA aboard at most, as well as one or more ships associated with the Recongregationists. The Recongs are (as previously established) associated with a radical group who had recovered the Koronus Expanse STC and have begun building a pocket empire surrounding it, with the eventual purpose (unknown to most of their agents) of destroying the Golden Throne and killing the God Emperor, so that he can be reborn anew and reforge the Imperium in accordance with the old ideals. The backing of the Recong Inquisitor, as well as cunning on their part, has kept this endeavour pretty much under wraps (as far as they know).
The upshot of this is that the party has the means and backing to support a small fleet of ships and will be doing RT style endeavours to expand the influence of their masters, and build up their personal influence, in cooperation with some Dark Angels of dubious character.
So the question is... how would this bastardy of a task group be organized?