Alaysian, what you're having troubles with is something that everyone has. The box is always going to be there, no matter what. For scenery, just swap a piece of scenery in the map for your new piece of scenery, and even though it's viewed as a yellow box in SE, it will show up in-game.
However, for vehicles, you'll need to do a meta swap in HMT. Not neccessarily with a piece of scenery, but you can do a vehicle too. Although if you import some unneccessary models and pieces of scenery that correspond with them, you can just overwrite those ones, and not have to replace any needed scenery/vehicles.
The odd thing is, on my first and second model import, the models actually would show up in Sparkedit... but, like you now, I get boxes... x.x If only I could remember what I did..
And as for the elites on the sides of the tanks, I can't help you there... make sure "Uses MC weapons" is selected, but other than that, I can't help you there..
