For example on an MD-88, is the center of gravity on the back of the plane because the empennage, wings and engines are located there? So they would have to put most of the cargo on the back of the plane?
Yes, the wing is positioned so that the center of lift is near the center of gravity. The MD-80 is very tail heavy due to the aft mounting of the engines. I have actually personally seen the nose of an MD-80 lifted off the ground by a jet bridge, and it didn't even hurt the door that was supporting the weight.
This chart is from the MD-80 weight and balance manual, which can be found on google. You can see that the center of gravity (CG) must be within -2.8% to 33.4% of the Mean Aerodynamic Chord (MAC) which is an approximation of average wing chord. So basically the CG must be in the forward 1/3 of the average wing chord, typically the center of lift is around 25% of chord. On the MD-80 the leading edge of the MAC is at body station 885.547, which is behind the actual LE of the wing at the fuselage.
The reason you want to place the CG near the center of lift is to create the smallest pitch moment possible between the CG and CL. The pitching moment created by the difference in the CG and CL location must be reacted out by the horizontal stabilizer. The more moment, the larger the stabilizer must be and the more inefficient the aircraft. Here is an illustration (stolen from this question How does a commercial airliner measure its weight/mass?):
Here is the picture of the MD-80 doing the wheelie: