Texture alignment:PLEASE align all of your textures. If you can't take the time to do this, don't even bother making a map. What I usually do is make an object, say a crate, where it's lined up on the grid (use a grid size of 64), then press Alt-L to lock the texture. Then you can move it wherever you want and not worry about having to line up the texture. If you do need to fix up texture alignment, though, hit "S" to bring up the surface properties. You'll see: S, T, R, SX, SY, which stand for horizontal offset, vertical offset, rotation, X scale, and Y scale respectively. Select the face you want to modify (click on it in the 3D window). Adjust the values, then click "apply face". Or, if you're doing something like a half-sized crate, put .5 in the X and Y scale, then press "apply brush" to apply it to the whole box. Negative values can be used on the X and Y scales if you need to flip a backwards texture.