You don’t say which version you are using but…
1. Have you tried Digital Anarchy’s Box Creator lite under the window drop-down that shipped with AE6.5? Great tool to create cubes and boxes quickly wothout calculating the positions of the layers and they’ll match up perfectly.
2. Depth to an image can be faked. Multiple layers set a few pixels apart in z-depth can work if you don’t take your camera directly on the edge of the layers. You can also construct depth using positioning and parenting all layers to a null object.
Also, make sure you composition settings are set to Advanced-3D in the Advanced tab of your comp-settings menu.
3. You can certainly import a 3D render with alpha channel and attempt to match up camera.Even import camera data depending on the 3d program used. Unfortunately I don’t know anything about blender3d.
4. A 2d layer as a background (like an animated starfield movie) placed behind your 3d layers will always fill your comp.
Good luck.
Don