Do the two sets have to have 50 numbers each?
No. It might be the case that one of the sets has several large numbers and the other has nearly all the small numbers, for example.

How much computer time can I devote to this?
For this assignment, the running time should adhere approximately to our usual 10-second rule for this input of 100 numbers. Typically, a lot more computer time will produce only marginal improvements, whereas a good algorithm-design idea will produce dramatic improvement. If you also experimented with an interesting method which requires signficantly more time but produces a significantly better solution, please feel free to discuss these results in your readme file.