With a million years with them, how did they ever managed to almost die?

There are probably two main things to consider:

1) Will's whole goal is to distribute as much time to as many people as possible. If he were to keep too much for himself, there could be someone, somewhere, who wouldn't have enough. Remember his line, 'no one should be immortal if even one person has to die.' Will had gotten used to living on just enough time, so he wasn't worried about it, and the movie constantly shows him giving time away (a trait he likely inherited from his mother ... she gave him some time in the morning even though she didn't have it to spare).

2) Will and Sylvia get a rush out of having very little time -- almost as if that's their way of knowing they're still alive.