In C1, find the folder where your photos reside. Right click then hit "synchronize".
Its gonna open an import dialog. There will be an "Import To" tab. Within that tab, you will see a "Store Files" dropdown. Pick "Current Location". That way it won't move your files. Thats assuming you don't want to move 'em.
If you move them, then LR will lose track of them.
As far as moving things around, I couldn't say.
I keep all of my photos in one folder, without any subfolders. That way, access is the same for both LR and C1.
If I import the images into LR, I'll then open C1 and synchronize, same goes if I import into C1 first.
My way may not be ideal, but it works for me.