Functional Connectivity with multiple subjects?

Hello, I'm a new user of REST and I'm trying to use the functional connectivity tool with multiple subject's data. I followed the instructions provided in the documentation but I have a question about inputting multiple subject's folders. What I did was selected one subject's folder containing their nifti pair data set. Then added another directory to the input list containing another subject's data folder. After starting the analysis I noticed that the Functional Connectivity tool created a FCMap and zFCMap file immediately after finishing the analysis of the first subject, the FC tool then continued onto the second subject's directory and upon completion it seemed to modify the existing FCMap and zFCMap. Are the results for the second subject over writing the results from the first subject or is this process combining the results at the end and that is why I'm seeing files created mid analysis and modified at the end? I just want to confirm that I'm inputting multiple subjects into the Functional Connectivity tool correctly in order to perform a batch FC analysis using all of the data. Thank you!