The problem with Boxes is that when you select the box set for the page, it will apply to all the boxes on the page. Having boxes in both the Morefoot and content means that you're cloning the boxes, which means, in essence, a duplicate set.
So, the solution I'd recommend is create your Morefoot box set, and go to Dashboard > PageLines > Page Options and click Site Defaults > Boxes. There, you can select the box set you want in the Morefoot to be a default, site-wide.
Next, get and activate
and use that, in lieu of our Boxes in content areas or sidebars. Boxer plugin replaces boxes with Content Blocks, also set up by sets, but applied to your posts or pages via shortcodes. The best thing here is that you can apply as many Boxer sets as you want inside a single page. I personally use 8 of them on my homepage, in addition to a row of Boxes in my morefoot.