Custom Field Form vs. Sidebar Taxonomy Forms Problem

I tried using custom fields to make a form for adding my listings in the add/edit page for custom post types because by default all the taxonomy choices display in the add/edit sidebar and its difficult to open each one up. However, this doesn't work as far as I can see. If you click/save items in the sidebar or the form they don't align in the saved data of the custom fields for taxonomy in the add/edit portion.

Any help would be greatly appreciated. Been at it for days with just issue after issue.