my trainer has a flywheel, and i think yours would too. to make sure the resistance is good, i put my pedal arm at 3 o'clock, and hold onto the flywheel. i then push down on the pedal hard. if the tire doesn't slip on the roller, then it's all good.

for the "standing muscles" issue:
try working on your core muscles, particularly your obliques. when you stand up and start cranking out HUGE power, your arms + core will give before your legs do. when you push down with your right leg you'll push the right side of your body up. you have to counter this with your core and arm muscles. to strengthen the obliques, you can do situps, lateral situps, or stick twists (if you have access to a reverse-incline bench). I recommend stick twists, but if you don't have access to the bench, you can't do 'em.