Your butt takes a few weeks to become conditioned, so dont worry, but if you get numbness then check your riding style and position.

With 3x7 gearing on a road bike, you generally ride in the middle ring most of the time, in the big ring with the wind behind you, downhill, or when you want to ride really fast, and in the small ring when you are battling uphill or against the wind.

Some people use their gears to maintain a constant speed, but I use them to maintain a constant power output and pedalling cadence, and just let my speed vary according to the conditions.

The best way of climbing is to mix 2 techniques of honking (standing on the pedals, using a lot of force) and twiddling (gearing down and spinning the pedals fast).

For normal riding, the brake tops should be in your favourite position. This gives you the option to go higher, or lower if neccessary.
Toe clips are fine for general riding. You need clipless pedlas to race, but dont worry yet.