Friends, here is perhaps as good an explanation on the Bus' aft engines as we can have for a show that is only 5 episodes old.
1) The Marvel wiki (and a few other online other sources) for the
Bus, note that the modified C-17 Globemaster III "aircraft is powered by 6 Pratt & Whitney F117-PW-100 turbofan engines." Further, they helpfully add that "the traditional vehicle has only 4 engines." Okay, that's nice, thank you, wiki.
2a) Say we throw out the real-world info of the wiki, and stick with available / official show material. I looked on the marvel.com but could not find any mention of the Bus. Oops, there went that approach.
2b) It does appear in the show to date that all six engines are the same appearance, size, and function, ie the aft ones are not something different (for example, only used for rocket-assist takeoff). Fine.
2c) Now here's the good stuff. The Bus blueprint seen often in Coulson's office on the show and and offered in the real world (derp!) at NYCC 2013, shows the engines all the same size, and one (an aft engine) has a representative notation. It's the only notation on that blueprint-y diagram for ANY of plane's the six engines. So, "in-universe" to-date they all appear to have the same function.
The engine note says "VTOL Ramjet Engine (TYF) [or does it say (TYP)? - I can't read those last letters. If someone has a paper copy from NYCC, please tell us.]
Whoa - how cool would it be to watch that Bus making ramjet speeds and/or especially VTOL movement (Vertical Takeoff and Landing)?! I'd love to see that thing go VTOL, moreso than that 1st episode's flying car silliness but up there with first viewing of the helicarrier rising in the Avengers film.
See for yourself (click for larger size):
Cheers!