There is not a great deal to see and do in Manado. When I went to Bunaken I ended up having to spend 1 night in Manado when I arrived and 1 night before I left. I guess I was only there for an afternoon and evening. I just went out to eat. Some good restaurants. Try Sate King, really cool restaurant with great sate at reasonable prices.
If you can time it so your flight gets in early then if I were you I would go straight to Bunaken Island.