avoid booleans as hell if you want to use the model in game

btw they are located in the bottom left menu bar, there's an icon with two spheres (one red one green if i'm not wrong) intersecating. Continuous press and you will get as pop-up 2 more icons for a total of three.
they are: object union (make one object out of two different objs), object intersection (make an object form the intersecating parts of two different objects, what is not intersecated will be deleted), object substraction.
now, right click on any of these buttons: you will get a little window with the booleans options: 1-triangulize objects if selected will make all the faces of the resulting object as triangles, 2-delete edges will delete all vertex, edges and faces that truespace consider not useful (even when they actually ARE useful), but i don't know about 3-"keep drill" and 4-there is also a parameter about booleans precision (note it will affect also the amount of edges deleted if this option is activated).
booleans may be of some help if you are making a model with game purposes in two different manners:
1- clear a triangulization using object intersection and delete edges on (create a big box that cover all your model then use this action)
2- make intersection. this may cause problems to your models, at least in fs2, (actually i've just made my fourth fs2 model with intersection without much problems but i'm a lucky man and it is known that this way may cause big probs to your model) just unify with booleans the objects when they are in a position that cause no intersection, then select one of the objects as group of face and move it in the right position.
there's another way to connect different objects if you are working with no game purposes: the hieracy (that is needed in a certain way also in freespace2 models developing). on the bottom right menu there are two icons (they are in a sub menu, so press some icons to see what you get): glue as sibling and glue as child. using them the two (or more) objects will be considered as only one, you can also save em as a single obect but you will be able in any moment to unglue them (use keyframe editor on the top left menu to see the hieracy tree)
if you are working with game purposes the best way will be a "face evolving" strategy: create a primitive, deform it, then use poly slice, slice section, poly bevel, polydraw, select faces, sweep, point editing, delete/add face, add edges and vertex and the other commands that i may have forgotten to modify a single objects obtaining something similar to your desired shape...but this strategy with truespace is true pain in the ***

...you may use those commands to connect separated shapes also...adding MORE pain to your poor ***

cya