Let me see if I recall some... Was that buried ship the missing part that kept the ship from leaving? Because, from what I perceived, it did not land beneath
the mothership (also the District 9 camp did not appear be be just below the "landing" site). And how come it took one guy so long to come up with a solution to "fix" the ship? Why did the aliens not work together. It would seem easier when they were up there and were not "dominated"
by the humans. Also, what was that cannister? Why woud a mutagen be required to run the ship?
Well let's see (mind you, this is just me remembering the movie and using lots of contrivances, not in any consulted from any source):
1) Apparently yes, that was sort of a "safe-boat-also-command" of the mothership, as for the exact locations, well movies, drama and all that jazz? :p
Or maybe they moved on to a safer place, so no one could find easily find it. And the District is a slum, slums are messy places;
2) Taking a wild guess (oh really? :p) I recall something said among the lines of "hierarchy" like insects, so maaaaaybe the one that fixed the ship perhaps could be the only engineer, mechanic or pilot. And could it be that too many aliens working on it, would have attracted too much attention. It's contrived, but I like that.
Also, something was said about their appearance being as of "lost" from the main "colony" (the words used are lost on me), so maybe without proper guidance of sorts, it took that really long to fix it. Which would also could be used to explain their inability to "rise against";
3) Yes, apparently it was some sort of mutagen that worked like a "DNA fuel" (saying that because of the Vikus mutation, but wouldn't explain why they didn't mess up with their own blood/DNA, so I'm using contrivance again)
with for ship. Remember that the guns and the "exoskeleton robotic thing" required alien DNA to function, so I'm going with that.