You have the right to travel with more than one child in a carseat. Whether you and your kids are comfortable sitting apart is of course a different story.
It's up to the airline to decide how to seat you all appropriately. FAA's official guidance on the topic (see below, excerpted from Advisory Circular 120-87B) gives a fair amount of leeway as long as "good judgment" is used. It will really depend on the seating layout and the opinion of the flight attendants, and this is a longstanding grey area, so it's hard to say what they will decide.
I would not bother calling the airline, because the phone reservations folks tend to know very little about operational details like this. If you send a specific question by e-mail, then there's a chance you will get an intelligent answer.
Seatguru is a great website for looking up the seating configuration of a flight, so that you can see your options for different flights and airports.
FAA: "TRAVELING WITH MORE THAN ONE CHILD. In the event a parent/guardian is traveling with more than one child in a CRS or is traveling with several small children, only one of whom is occupying a CRS, good judgment should be used regarding placement of the CRSs As long as these conditions below are met, the CRS could be placed in a seat other than a window seat. At a minimum:
• The CRS should be placed so it does not block any passengers (including the parent/guardian) egress to the aisle used to evacuate the aircraft, and
• The CRS should be placed so the parent/guardian can reach the child in the CRS to release and evacuate with the child, should an emergency evacuation be necessary."