Select the whole model and change its mass to some arbitrary weight, like 100.
Open the model's GeoLOD.
Create 4 cubes at the extents of your model, give them each 1/4 of the mass that you want the whole vehicle to have. Let's say 2000 kg- so each would weight 500. It is not really very important how big these things are. I would make them probably around 10 cm or .25m in length/width/height. Make sure to uncheck the option that will try to keep the total mass of the model the same when you're adding weight. While you make them it might be a good idea to create named selections for them so you can grab them easily if you need to. From the top menu, select structure\topology=> find components.
Now, move the weighted cubes around so they affect the mass distrution of your model. Check your changes in the flight model, come back and retweak, etc etc.