Hello,
1. You need to apply a module class suffix of -no_padding to the module in it's backend to remove the padding. A listing of the suffixes can be found here:
http://www.shape5.com/demo/shenandoah/index.php?option=com_content&view=article&id=14&Itemid=49I would recommend doing the same thing for your accordion menu as well.
2. I am sorry I am not sure which menus you are referring to? What is the exact text in the menus so I can identify them?