Menus not working correctly

First, thanks for the great theme, really nice and easy to work with. I have recently started adding more pages to my site and as such my navigation menus have increased. I have tried nesting the menu’s etc, but I only get single links in the top nav (missing a number of pages there as well) and the side nav all the pages are listed but would like to have more of an accordion or mouse over menu pop up for the nested pages.

So first, is there a recommended way to use this theme with a large amount of pages in regards to menus? Second, is it possible to make accordion or mouse over type menu’s in this theme?

Thanks