There's several things you might want to decide before diving into this.

First and foremost, you need to decide on a reason. Why are the aliens doing this? And then, you need to decide on a method. How are the aliens doing this? And, lastly, what's their stance on humans. Are they food? Labor? Both? Neither? Incidental or irrelevant?

Once you've answered these questions, you can start designing your alien race - or races, for that matter. You don't need to go into too much detail right now, but you do need a firm idea of technology level, typical method, how they look, what their culture is like - and you can start thinking about whether they're a monolithic culture or whether there's factions with the aliens that don't want to invade.

Then, you need to close in on your gameplay.

Which part(s) of the invasion do you want to play? Is it the initial phase - maybe there's an infiltration phase, like when the Skrulls attacked (which they've done repeatedly in the comics), maybe the aliens build a superhero team and start to do heroic stuff to gain a foothold in the setting - or maybe they're arranging for apparent heroic stuff; being on both sides of the table, so to speak.

The all-out war phase needs to have identifiable objectives - a way of keeping score, and to see whether you've 'won' or 'lost'. All-out battle isn't where tabletop roleplaying games shine - though it works with games such as DCU Online or Champions Online or Freedom Force or Kill All Humans, it just isn't conducive to tell a story for players around a table.

Then, there's the mopping up phase. When the aliens have won (maybe), or have severely reduced holdouts in the setting. Maybe the aliens have gone to ground, and you need to lure out superpowered aliens in order to defeat and contain them.

And, then there's the budding rebellion phase. If the aliens won, then you might want to start play in a world where young heroes get their powers and start to fight the aliens again. If the aliens lost, maybe the aliens got enslaved and the players are playing aliens with powers.

There's many comics and movies that deal with invasion type stuff. Skrulls are notorious for doing this. Then, there's the Chitauri invasion in one of the Marvel movies. Just to mention two. One interesting and less well known comic might be Strikeforce: Morituri, which has a unique take on this.

You've got movies like They Live!, or Buckaroo Banzai, both of which are cult favorites. Even Charlie Sheen has one invasion movie, in the form of The Arrival from 1996.