As for your legs and knees hurting, I can’t be sure without actually seeing how you look on the bike, but I have a couple of guesses of why your knees and legs would be hurting. Your knees are the most important thing, so if they are hurting do something asap. If your knees hurt from behind you are probably too high. Have someone hold your handles while you clip in and cycle backwards so you can focus on how high you are. (Even a cm can effect how your legs feel.) Make sure that you are high enough that your legs are almost straight, you don’t want to lock out.

Also think about how far back your seat is/the angle it is. Give it some time though, if you are just starting out your legs are going to be tired and sore cause you aren’t use to it yet. Still they shouldn’t be falling asleep or anything like that. Good luck with the biking and the commuting. And thanks for the tip with the Camelbak, I’ll get my hands on one and test it out. Let me know if you have questions, if I don’t know my bike shop guys will.
Cheers.