I pedal up inclines all the time with the motor running....I would not do it any other way. I've tried to go up hill without the motor and did not get very far..I do have a single speed which makes it much harder.
One of my main reasons for motorizing my bicycle was to get some exercise. I pedal mine almost all of the time and only use as much throttle as necessary to maintain speed and for hills. Pedal as much as you want... the only side effect will be to increase your MPG!