kinda hard to tell what you are saying with that small bit of info, but here is what I can offer on just basic texturing techniques.
Your texture alignment doesnt not automatically align to your brushes. Sometimes you may be fortunate/plan ahead enough to use textures that just happen to be the correct size as your brush for instance a wall 128 wide or long X 128 high, with its point of origin on 0 in the z axis.
This would align properly if the brush was in the just right place and you were using a texture that was 128x128.
Soooo if you were to use a texture, let's say was 64X64, it would appear that it was tiled 4x on that 128X128 brush forementioned. If you used a brush that was 32x32...16x tiles.
You will need to either adjust the x or y axis of the texture manually until it aligns to your liking.
You will need to scale it to your liking using both the x and y axis as well if you want to manually do this. Really good for texturing parts of a texture visibly.
other things you can do is use the justification buttons in VHE, (right left top center bottom).
If you want to just stretch the image to your liking, use the fit option, but bear in mind, that stretching textures more than 2x or less than .5x is not recommended. If you do too much stretching and fitting you can get some really odd luminol errors etc.
and lastly sometimes you need to rotate your textures. Keeping it simple, lets say you have a nice symmetrical map thing goin on. You make a giant toilet prefab and texture it, looks all great. You want that same toilet elsewhere, so you clone it, spin it 90 degrees. You will note that the textures are still at the angle of which you first created and textured it. You will need to use the "rotation" option in the texture tool and enter 90 degrees and click apply to get those textures looking the way it did beforehand.
Hope this helps ya some, if you managed to actually read it all