Not sure what you are asking. Layer switches are exclusive for the most part and except for the layer quality setting none of them ripple through to sub-comps. That's the whole point of those switches - to control layer appearance selectively. For your timing problem you might simply consider stacking the two timelines or using comp markers in teh pre-comp, which will then become layer markers in teh main comp. They do not interactively update, though. also simply consider using more pre-comps to streamline the toggling of al lthis stuff. Sounds like you are simply trying to do too much in as few comps as possible...
Mylenium
