This sounds like a standard 2 plane rigid rotor balancing problem. With the proper balancing machine, it will tell you exactly how much weight to add to each end. If you are doing it the "old fashioned" way without a computerized machine, it is still not all that difficult, providing that you can get accurate readings for amplitude and phase angle at each measurement plane.
The general the method is as follows:
1.) Do a trial run in the existing condition and record both amplitude and phase angle for each measurement plane.
2.) Add a trial weight to correction plane 1. You must record both the weight and its phase angle. Spin the rotor and record amplitude and phase angle at each measurement plane.
3.) Remove the trial weight from correction plane 1 and install it on correction plane 2. Spin the rotor and record the amplitude and phase angle at each measurement plane.
4.) By using the results of #1, #2, and #3 above, it is possible to solve for a 2x2 complex matrix of influence coefficients. Polar notation is most useful in expressing the complex numbers. The matrix equation is A*x=B, where A is the 2x2 influence coefficient matrix, x is the 2x1 correction mass vector, and B is the 2x1 vibration reading vector. A, x, & B are all expressed in terms of complex numbers.
5.) After completing #4, set vector B equal to 0 and solve for vector x. The resulting vector x gives the correction mass and phase angle at each correction plane.
I hope this is helpful.