As a newbie, you're not understanding how the texture editor works, and that's why you're so perplexed.
But, it's pretty simple once you know how to do it, and once you understand "how the TCE works".
Starting from where you are now... go back to the viewports and, in surface selection mode, only select the surfaces on ONE SIDE of your cube; one of the sides that is NOT textured properly.
Now, return to your TCE viewport. Click one of the buttons to reassign those surfaces to be viewed from a different perspective. That is, if you originally selected "front" for your texturing, select "Left" "Right" "Back" or bottom.
Notice what happens in your TCE viewport. The green-shaded shapes will likely change a lot*. And you'll notice that only the SELECTED surfaces appear in the TCE.
Return to your modeliing viewports. The side of the cube will be textured differently.
Here's what you're not (yet) understanding: when you select
an entire object and try to texture it, you initially select one perspective from which AC3D textures the part. Surfaces not perpendicular to that view angle (that is, 90 or 180 degrees from it) will not be textured as you want because the viewing angle is so acute. However... the TCE allows you to selectively assign the proper perspective for any single surface or set of surfaces, so: in the case of a cube, you assign the surfaces on the top of the cube from the Top perspective... those on the left from the left perspective, etc.
What you've described is simply discovering that, for example, the left side view texturing "doesn't work" when the cube is textured from the front perspective.
The 2D graphic you use to texture the entire cube won't move vis a vis the TCA screen.... you will manipulate each of the surfaces for the various sides to fit the part of the graphic that is meant to texture them.
I hope that makes it a *little* clearer.... if not, send me a PM. If you have Skype we can arrange a time to meet and I can clarify it for you inside of 10 minutes!
*I take that back: your object being a perfect cube, it probably looks the same, increasing your frustration. Suffice it to say, if the object were not symmetrical, you'd be able to see this....