So what exactly pitches the plane upward with the rear end down? Do flaps help lower the nose when deployed 80%-100% down with such low speeds?
The change in pitch during the landing is called the flare and it is controlled by the pilot (or autopilot for an autoland) using the elevators (i.e. pulling on the yoke). From the Boeing 737 NG FCTM (6.10 Landing):
When the threshold passes under the airplane nose and out of sight, shift the visual sighting point to the far end of the runway. Shifting the visual sighting point assists in controlling the pitch attitude during the flare. Maintaining a constant airspeed and descent rate assists in determining the flare point. Initiate the flare when the main gear is approximately 20 feet above the runway by increasing pitch attitude approximately 2° - 3°. This slows the rate of descent.
After the flare is initiated, smoothly retard the thrust levers to idle, and make small pitch attitude adjustments to maintain the desired descent rate to the runway. Ideally, main gear touchdown should occur simultaneously with thrust levers reaching idle. A smooth thrust reduction to idle also assists in controlling the natural nose-down pitch change associated with thrust reduction. Hold sufficient back pressure on the control column to keep the pitch attitude constant. A touchdown attitude as depicted in the figure below is normal with an airspeed of approximately VREF plus any gust correction.
The flaps are set much earlier during the approach phase. They are not changed any more during the landing phase.
Flaps help to increase the lift at low speed, allowing the aircraft to fly at a lower than cruise speed speed.
The pitch up is caused by the elevator on the rear wing.
For landing an airplane has to slow down. When looking at the lift equation,
We find that, to get constant lift $L$ with lower speed $v$ we need to increase either $c_L(\alpha)$ or wing surface area $A$ (we can't change the air density $\rho$).
Note the explicit dependency of the lift coefficient on the angle of attack $\alpha$. We can increase the angle of attack by pitching up, which is why planes generally have a nose high attitude on landing.
Flaps change either the lift coefficient for constant $\alpha$, the wing surface area, or both. This helps to reduce the required angle of attack, so the the pitch attitude may be reduced as well.
I don't know if your question relates to the approach phase or the flare. The later as explained above has to do with the elevator, the former i.e for the approach phase you will notice that airliners and even more so fighter jets come on the approach indeed with a high noze up attitude. That has to do with swept wings. Swept wings allow an aircraft to fly faster by retarding the speed at wich the wings will become supersonic. That's all fine, but the problem with that is (amongst other ones): it will reduce the lift generated by the wing therefore forcing the aircraft to fly at a higher angle of attack during the approach. Hence the noze up attitude of the plane during that phase.