Sync and merge clips, proper ways and tips please

Hi
Im working on a indie feature and need help with sync and merging clips. So far from my trials Premiere doesn't really sync that well based on audio (plus it doesn't seem to sync more then one set of clips at a time), luckily I have Pluraleyes that syncs in a breeze so that's what I'm using. So, my questions:
1) How do I merge more then one set of clips simultaneously. Look at my timeline. This is from only 3 days of shooting (and we've shoot for 33 days). It will take me forever to merge these...
2) How do I merge clips so they end up in a specific bin in the project panel. Now when I do it the new merged clip ends up at root which is manageable but annoying.
Can someone confirm if this is actually how you work, very laborious or am I missing something?
Thanks!

I'm dealing with the same issue, and would love to know how you've solved this problem, assuming that you kept this same workflow going. 

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