I use Tom's online calculator at
http://runfastcoach.com/calc2/index.php
. In cross country season, I use our kid's current 5K times, adjusted for the course, etc. For instance, if the kid runs a big 5K pr on a flat fast course, and we are going to run CV reps on a hilly course with thick grass, I know that the times probably should be a bit slower. Also, it is important to take other things into account when assigning paces, such as stress levels of the kid, fatigue, weather, whatever. I just usually tell the kids before we train, "On a perfect day where you are feeling good, this is your pace today. If today isn't a perfect day, we will adjust." Or a couple days ago, we had 25 mph wind gusts so I just said, "Don't stress over the times too much. You know what CV effort feels like, just do the best you can today." The workout went great and they actually hit the times without trouble. Might be time to bump their times up a little, but we will see after they race this weekend.
In track, if I have kids who are reasonably well balanced across events from 800-3200 meters, I use their 3200 time. If they are better at the shorter races, I would fudge their times a little when I use the calculator, because using an 800 to calculate CV pace isn't the most accurate and usually ends up producing a CV time that is a little too quick. I can usually tell just watching the kids if they are running CV effort and will slow them down if it looks too hard.
I think running a 2400 meter time trial would probably be a good compromise distance to determine CV pace for 800/1600 kids who are not your distance standouts. However, I don't see a 2400 meter option on Tom's calculator for you to plug into. He does have a 1.5 mile option which would be close and you could estimate.
Tom also has some formulas he uses to calculate CV for kids who are skewed toward the shorter events, using their 400, 800, and 1600 meter times, and he shares these in his coaching DVDs and probably in clinics he does. These methods work really well I think, but I don't feel I should share them without his permission. You also might be able to find some other ways to estimate CV pace on therunzone.com board...and this will get you very close. There are tons of very useful threads there on training.
I adjust my kids' CV paces as they get faster in races during the season. Since I always give them a range of times, this isn't much of a big deal- they just sort of naturally start moving towards the faster end of their range as they grow more fit, and then we create a new range of times if their race performances indicate we need to do that. You can also progress their CV workouts by shortening recovery time or jogging the recovery a bit faster (same thing for most kids, since almost all of mine jog recoveries), lengthening the reps, increasing the total volume (to a point), etc., just like any other interval workout.