i am just the opposite of you. my "standing up" riding is much better than my "sitting down" riding. i can run the pace of the slower pros while im fresh and standing up but when i tire and start sitting im running the pace of the novice riders!!
a couple of tips i have is dont be afraid to move around and work your bike underneath you as you are standing, alot of people tend to tense up and not relax when they are standing. also, if you notice your hands and arms getting tired quickly, you probably arent leaning foreward enough. alot of people preach keeping your head above the number plate when standing, but its really more about keeping a neutral balance point and letting your legs do the work, which means under acceleration you would be leaning foreward more than you would at a constant speed and certainly more than braking.
one little trick i do when practicing and riding slower is to take one hand off of your bars while standing and rolling through some turns smoothly and slow.
it wont take but a second to determine if your positioning is neutral or not.
hope this helps...
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