Sure thing. You do that by using null objects in XSI (Primitive->Null). There are some naming conventions to be followed in order for the converter to recognize them though:
First add a null object called "rootpoint"
Then add nulls for "Center", "Above" and "Aura", after that you can add nulls for "Exhaust" and weapons, called "Weapon-0", "Weapon-1" etc.
However, since the converter strips the first five characters from the name of a null object, you have to name them so that there are any five characters prefixed to the name. So instead of "Weapon-0" you would name the null "aaaaaWeapon-0" or like I do "000-Weapon-0", "001-Weapon-0" etc. (only four characters because XSI automatically adds a "_" in front of a null name which begins with a number). This is also useful for having multiple nulls named the same (for example multiple hardpoints for the same weapon, or multiple exhaust points) since XSI does not allow two objects to have the same name.
Once you are done adding and naming the nulls, you have to open the Explorer (Alt-8) and drag all the nulls to the "rootpoint" null. Select them all along with your model, export and convert. That's that.