In using Eclipse dragon, it states - if you control 4 or fewer runes, draw 1. My question is the exhausted runes include the controlled runes or the awaken ones are the only control runes you need to count?

Yes — exhausted runes count. "Runes you control" means all runes on the board you channeled, ready or exhausted (Rule 191.3).

Exhausted is just a state on the board (Rule 414.2) — it doesn't change control. So if you have 3 ready and 2 exhausted runes on the board, that's 5 controlled runes, and Eclipse Dragon does not draw you a card. Only runes still in your Rune Deck are outside your control and don't count.