Havan, also called Yajna, is a Vedic ritual in which people put on a fire in the center and make offerings along with chantings of mantras, mostly to please a god/goddess and/or achieve a certain objective.
Though nowadays these Yajnas are of relatively lesser length of time, earlier and as per mythology these could be long and difficult to complete, due to which a Yajna or a Havan is a symbol of dedication and hardwork for an objective.
Havan Kund is the center place in a Havan in which the fire is put on and all the offerings are made. It could be considered like a sanctum sanctorum for a Yajna.
For the meaning of the song Havan Karenge from Bhaag Milkha Bhaag, check HERE.