I was able to load a fleet and start a challenge… only when I got into the game did I realize I had deployed twice the points as my opponent
Do you mean cost of fleet or the bar at the top of the screen where it also lists what percentage of your fleet still exists? If it is the latter, I think that refers to weight or something. Such that, if the challenge have few or no cruisers and a lot of frigates/fighters, and you have the opposite, your weight would be much higher.
Hmmm… Maybe I am wrong. It just seems like it wouldn’t do that before… i.e. we would have 25000 and his fleet would be that, but I was able to start with 37000
Check his fleet composition. I know that I have run fleets well below and well above the opposing fleets mass or whatever that represents. Also, check here : viewtopic.php?f=24&t=3237
My usual survival fleet is 10000 plus, but with only frigates, the mass (or whatever it is) was well below 5000.
Odd… well maybe I just don’t get how it works. then 
I must also admit to be frustrated with the challenge interface… I can’t seem to find where to create a new challenge from scratch. All I can see how to do is to respond to an existing challenge by creating another challenge using the same map/rules. I don’t know how to modify the rules.
I don’t know. One guy in the modding area did… There should be something in there about how to… if there isn’t, it would be worth tossing up the question.
Those numbers are the total hitpoints of your ships. It’s done this way because hitpoints basically represent how much of your fleet is remaining.
Two fleets won’t necessarily have nearly the same amount of hitpoints. Some fleets will use lots of armor and other things with hitpoints, whereas others will stay light, fast, and try to rip the enemy apart faster. If you think of it like a fantasy RPG, the warrior has more hitpoints than the mage, but that doesn’t make the mage less useful.
The total hitpoints a fleet has doesn’t really indicate how powerful they are.
That last post is spot on.