I tend to stay submerged for the majority of the time I'm patrolling. I only surface to recharge the batteries or chase down a contact. It takes longer to get about, but you end up with more contacts to make it interesting, and plenty of fuel.
I normally aim to spend the entire daylight hours submerged. After nightfall I'll surface and recharge. While I'm doing that, I'll drop down to 25 meters every 2 hours or so for a half hour sweep of the hydrophones. By daybreak the batteries are full, and back down deep I go.