Henry, one thing you always need to keep in mind; layers don't separate geometry in SU at all - they just control visibility. Therefore if you have basic ("primitive", "raw" - i.e. ungrouped) geometry within your model, you shouldn't put different parts of it on different layers because these parts - though on different (sometimes hidden) layers - still interact with each other. See this video for basic ideas and mistakes to avoid:
[flash=425,344:3m1el3he]http://www.youtube.com/v/fBdP499iw0Y&hl=en&fs=1[/flash:3m1el3he]