How do I stop block menu from showing all levels of the menu?

I am using adaptive theme and I built a three layer main menu using the primary menu option in my theme plus menu block. It was great. But then I realized I needed to redo my menu so that it was one continuous Ul LI type structure because I'm trying to integrate packery into my site.
Here is a demo of my menu as "menu blocks" here: http://dmta.right-brain.com/our-work

I found this Packery code by looking at other sites that use packery:

// Filter projects on work page and reset packery layout
	if( $('body.page-template-page-work-php').length != 0 || $('body.tax-project-category').length != 0) {
		$('#nav li#menu-item-20 ul.sub-menu a').not('#nav li#menu-item-20 ul.sub-menu a.expand').click(function(e) {
			e.preventDefault();
			$(this).parent().siblings().removeClass('current-menu-item');
			$(this).parent().children('ul').children('li').removeClass('current-menu-item');
			$(this).parent('li').addClass('current-menu-item active-link');
			var splitUrl = $(this).attr('href').split('/');
			var slug = splitUrl[splitUrl.length-2];
			var total = $('.project-list li').length;
			if( slug == 'our-work' ) slug = 'item';
			$('.project-list li').show().each(function(i) {
				if(!$(this).hasClass(slug)) {
					$(this).hide();
				}
				if(i == (total - 1)) {
					pckry.layout();
				}
			});
			verticalCenterHeaders();
		});
	}

It does this thing where when you click on "Our Work" which is '#nav li#menu-item-20 It filters all the projects that are children onto one page and lets you narrow them down by type depending on what taxonomy term you click on from your menu. So like, if I click on "restaurants" it filters to only restaurants with out me leaving the "our work" page.

So I don't know what to do. I rebuilt my menu using the block menu and it seemed like it would work better, until I realized, something. How do I turn off menu items that go down too deep in the menu tree, the projects themselves. Like "Demo place one" and Demo place two" show up on the menu under my taxonomy subcategories whether I like it or not.

Do I go back to my old block menu way of doing things and re-figure out how to do packery or do I try to stop the block menu from going down further than I want in the tree?

I really need some help, any input would be great.

Rebecca