The game engine has been using the 2-point conversion chart listed here: http://www.theredzone.org/Features/TwoPointConversionChart.aspx with a few minor modifications that made more sense to me. Today I have released the ability for you to control your team's 2-point conversion decision making! This is under "Misc Gameplan Options" in your gameplan screen. There are two sections, one for when to go for 2 when you are ahead and one for when you are behind. You will still only go for 2 in the 4th quarter, but now you have control over when that happens.

Can't you already do this with rules by selecting Extra Point as the down, and then selecting offensive formations like normal?

yes, you could do that if you wanted to go for 2 when the game engine would have gone for 1, but you couldn't prevent going for 2. You will also still need to use rules if you want to go for 2 before the 4th quarter or want to have more control over it; you can also now only go for 2 by the rules by turning off all 2 point selections. (Rules still override this selection)

Does it go for 2 the whole 4th qtr? Or can you set it to go for two under a certain amount of time to go?

It's the whole of the 4th quarter. You can get more granularity via the gameplan rules of course.