So, how does invasion work in a system with two planets. You activate the system once and must attack immediately according to the rules so do you invade both planets at once or come back on you next go around?

Once you have won the space combat, you have to decide your planetary landing, as can be found in page 12 of the rules.

See here:

"5) PLANETARY LANDINGS
After any Space Battles are completed, the active
player may now commence Planetary
Landings by landing Ground Force
and PDS units from his Carriers
onto planets in the activated system.
If a system contains multiple
planets, the active player may
split any landing forces between
them in any way he sees fit, but
may not change his mind once
the Invasion Combat step
begins.

Then if you decided to land GF(Ground Force) on more than one planet, you then initiate a invasion combat process for each of the different planet you are invading.

Hope it helped.

Ugluk

InvestFDC said:

As Ugluk said, space combat and ground combat are two separate phases. You must engage in space combat if enemy ships are present when you arrive. Assuming you win, you may then CHOOSE how or if you will deploy whatever GFs you have with you among any planets in the system. Every planet you send GFs to will then have its own Ground combat phase. You are not, however, obligated to send down GFs to ANY planet, even if you have enough. You could choose to blockade the system without invading any planets. (Granted this isn't what happens in practice, but it's an option. =P)

Also, note that you have to declare your invasion parties for both planets before resolving either. IE, if you have 2 planets, and 6GFs to land, you can't say "I'm going to land 3 on one, and then wait to see what happens before I decide what to do with the other). You must announce what is landing where FIRST.

This mostly becomes important with Distant Suns counters, but can have implications at other times.