The % Compare indicator shows the relative performance of symbols that you compare to your chart's focus symbol. It creates a baseline, i.e., your chart's focus symbol, around which all other stocks, mutual funds, and indexes are compared.
For example, if you apply IBM as your focus symbol and then in the "compare to" section add MSFT, the % Compare indicator will display IBM as a flat line in the middle of the indicator window with MSFT's performance plotted relative to IBM.
If MSFT's line rises above IBM, it means that MSFT is outperforming IBM. If it falls below IBM, it means that MSFT is under performing IBM.