Whilst MI5 concentrates more on internal security, they should be working outside of the core Bretonian systems, the Tau's, Omegas, Omicrons and independent systems ( cortez,magellan). gathering info and warning BAF and BPA of imminant attacks from the bad guys and approaching smuggelers. They are tagged (gaurd iff as well so more or less in your face) and would be seen as the first line of defense and intelligence.
MI6, on the other hand, work behind the scenes in almost any other system you care to mention. Working closely with BAF ( since MI6 is the military arm of intelligence gathering and other dirty low down stuff:)) and the Priveteers to fullfill thier mission, whatever it may be.
This is how i see this working. The opportunities for some really good rp is boundless.