I'm assuming you have this all within a while loop and a timing factor of some sort which acquires the data at set intervals. One way you could do this is creating another loop that reads the data from the files after the data is written to the file and then do the combination of data that you need to within the new loop. Once you have the additional signal with the RMS value of the six channels you can save it to a new file all on its own.
I recently did something of this nature. I had a 5 channel board reading a light sensor for red, blue, green, cyan, and yellow light. Once I had the individual voltage levels I had to do a combination voltage reading afterward and save it to a text file. It's actually quite simple when you break it down step by step..