First of all, before you board the plane ask a person at the desk if the flight is full. If it isn't, you should be able to bring both car seats on board and have a place to secure each child. If your airline has pre-assigned seats, it should be easy enough to find out if the seats next to you will be available. Paid-for seats are great, but those wonderful empty seats are priceless. ;-)
If the flight is full and/or the seats next to you are taken, you can still bring the extra car seat with you right up to the gate. I know it's a pain to drag it around the airport, but when they check it at the gate, it's really well taken care of and doesn't get tossed around with all the other baggage. When you disembark at your destination, it will be waiting for you right when you step off the plane.
Another benefit of checking at the gate is the fact that you'll HAVE the chance of bringing it on board with you and snagging that extra seat, as I mentioned earlier. If you check the car seat with your other baggage (or if you leave it behind altogether and opt to rent) you might be kicking yourself when you sit down on a half-empty plane.
And having flown both with and without car seats, I can say that I personally MUCH prefer having a (familiar) place that my child can be strapped into and possibly even sleep in. All my kids want to do when they're sitting in my lap is squirm off! :-)
Good luck!