Your main menu can be 1 level deeps links to content. You just maintain these links as your top level content links as needed in the Menu configuration page.
For each main-menu item, make a new Menu where you actually set the link from your node edit pages.
Use MenuBlock and like the Context module (or just default the Block UI, eww) set each sidebar menublock to appear for the appropriate main-menu url path.
-- OR TRY --
You can try to make main-menu your site tree of all links, then use 1 menu-block set to 2-level deep starting point based on the url path.
I usually try to do the 2nd option .... then find its inflexible at some point and need a collection of menus and menu_blocks as I first described which from experience works better. Especially for cross-linked content (you may get the wrong menu block in the 2nd approach, for cross linked content as it shows the first menublock that menu_block finds the link within).