yup, just find your "split hierarchy" button (its under the "glue as sibling" or "glue as child" tab, it will be either or depending on whatever was selected last) to separate all your cubes to individuals, and you can go about this one of a few ways:
1) take all your cubes and glue them together as siblings, so your trueview archy will look like this
+model's hull <rename this though
cube
cube
cube
local light
all you have to do in trueview is drag one cube and drop it on another to to create a new group, and then drag and drop all other cubes and finally a light into that group. PCS will recognize this single group of multiple objects as you fighter.
while this is not really good modeling practice for fighters, it does sometimes come in handy. it is also good for hunting down any bad geometry. if PCS hates the model you can remove 1 piece at a time to see which piece it hates.
2) object union, found under your boolean operations tab along with object subtract and so on. this more or less welds separate objects into one solid object, so cubes 1-12 lets say becomes cube1. if you do this the objects cannot be separated from each other so its wise to save before you do this and save it as a different model afterwards like "fighter" and then "fighter1", that way you can go back and fix things if they get screwy on you and it gives you a more raw version of the model so you can go back and remove or change separate parts later. a note on unions, TS can be finicky about this and unions of complex geometry have been know to cause hassles with PCS and ingame. I've had a few issues with this, but over all nothing catastrophic that made me have to toss a model, then again thats why i save the model pre-union, so if a union does go wrong, you can go back and correct it. you just have to play trial and error with this one.
3) Extrusions, slicing, sweeps and bevels. these are what you use to create object extensions you would otherwise union to the model later. this can be time consuming and irritating yes, but the advantages are this, rather than mating two pieces together, you are sculpting and bending one solid piece, so virtually none of the issues of boolean ops arise this way, and often or not you can achieve much better results using this method.
drop in a cube or whatever and torture it with this method and see what you can come up with. but as far your model is concerned, which i gather you dont really want to delete any geometry, try options 1 and 2.
yup, to much coffee in the morning makes me hammer out stuff...
anybody correct me if i am wrong or left something out.
hell, im not even sure if this post was necessary. if it helps any, COOL!
