First of all, if you have a .obj, MC schematic, binvox, or VRML file, then SMEdit will take all of those perfectly fine. Since you have a .obj, just forget about the entire binvox thing. As for SMEdit, you can get it here:
SMEdit. If you're trying to figure out how to run it, try here, as it's been quite some time since I originally installed it:
SMEdit - StarMade Wiki.
Once you have SMEdit working, you can import your model into it by going to File> Import>.OBJ, at which point you can choose your .obj file. The next dialogue box will give you some options, just make sure that you specify the length you want the ship to be. At that point, you should have a grey ship-like blob in the display, you will then want to use the hollow command under (I forget, it's in one of the menus up top) so that you will then have a hollow shell to work with ingame instead of some three million mass chunk o' hull.
You now have a hollow ship shell, but... it might be in the wrong direction, or the core is outside the ship completely. Both the commands to do this, move, and rotate, can both be found in the same dropdown menu that hollow is found in. If your hull color/block is unsatisfactory, go to the "plugins" menu and choose replace blocks, or something like that. If you're happy, go to File> Save as > blueprint. Then go ingame and find your ship in the catalog.
A short note on system requirements:
32 bit java+1 gb ram will easily let you do anything under 300m. Bigger stuff will usually require 64 bit java+ a lot of ram, you can change the ram amount in the SMEdit launcher- note that you cannot allocate more than 1 gb with 32 bit java.
