I would like to ask if someone knows how you can make the panes(for time in out and layer switches) would stay the same through the whole project. Right now i have to manually switch a lot of stuff on or of because i have a heavy nested comp and i always need the in out times and layer swiches. I set it up in the main comp but it wont reflect onto the other comps. which is good in its own right but right now its just a pita. I couldn't find anything in the preferences nor the forum.
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...
What are you referring to? The column layout? This is automatically inherited for every comp you create fresh and it obeys your last setting. There's no way to re-arrange the columns post-facto in all sub-comps just by changing it in the main comp. It's a per comp setting.