They aren't really "alternate ending" in the sense that the story deviates at a certain point in the main story. It's pretty much a totally different universe (it's called "Another World", afterall), where Tomoya never meets Nagisa (or at least never bothered to help her; either way, she has not part in the these stories at all). You can watch the OVAs whenever, as long as you've watched to the point where they've been introduced well enough in the main story (which is probably at episode 18, actually, since from now on, it's pretty much only Nagisa centric [aside from mini-arcs centered around the even more minor characters in S2]).
But nonetheless, it's fine watching both of the OVAs after both seasons.
Edit: Oh, right; Steel's right. You can/should watch both OVAs after S1, with that "comic relief" mindset going on...
(Although Tomoyo doesn't really do anything in S2. Kyou does, though...)
Edit2: Just watch them in the order that they were presented: S1 » Tomoyo OVA » S2 » Kyou OVA
That way, there's no argument...