Fun ship designer bug
Weeeee
from
GalCiv2 Forums
I think the computer is abusing this, so you should too 
Go into your options and disable "remove functional when upgrading a ship design" (as in leave the check box blank)
Go design a ship by "upgrading" an existing design, in my test case a Yor colony ship (I wanted it to look like the original, I just wanted new engines), and have fun
I was able to fit 6 Ion Drives (they only used 4 capacity each for some reason???) and a whole bunch of life support on mine in addition to whatever it started with before I began adding things (colony module, 3 life supports)

Go into your options and disable "remove functional when upgrading a ship design" (as in leave the check box blank)
Go design a ship by "upgrading" an existing design, in my test case a Yor colony ship (I wanted it to look like the original, I just wanted new engines), and have fun

I was able to fit 6 Ion Drives (they only used 4 capacity each for some reason???) and a whole bunch of life support on mine in addition to whatever it started with before I began adding things (colony module, 3 life supports)