Hmm, it seems to be that I can either have the SH game influence the BFG game, or do it the other way around. I was kinda hoping to find a way to have the two games run parallel to each other, but time wise that would be almost impossible. I mean, a turn in Space Hulk would be a couple of seconds (minutes at most) in 'real life' (for the units that is), whilst a turn in BFG could last several hours.
An idea could then be to play the game of BFG, but once you have boarded an enemy ship, the game switches to Space Hulk/Zone Mortalis/whatever. Since each turn in BFG symbolizes a couple of hours, a complete game of Space Hulk also does that (all the turns put together). After the game of Space Hulk is done, the BFG battle continues as normal (of course counting in the effect of the SH game).
It would almost be as a campaign, but it's a single BFG battle, with multiple smaller battles (boarding actions, dogfights, etc) in it. Perhaps even use Aeronautica Imperialis for dog fights (would need different stats though).