The deck builder can tell if you built an EDH deck. But, Is there a way to separate your Commander/General within the decklist? If not, there should be that feature

There isn't a way to separate out the commander, but you can (this pay be a premium feature, idk) set a note on the commander so it stands out. Example

They have now added the new feature to declare your Commander / General which is welcome but lost the ability to search public decks by the format (EDH / Commander) and subformat (e.g. Tiny Leaders ..). EDH decks now show only as Legacy (well usually depending on the cards used) no matter how they are declared as by the user. I expect this to be fixed soon.

A toggle to show only 60 card decks or 100 card decks, with / without sideboard would be a help filter as well.

http://deckbox.org/decks/mtg