How can you calibrate extrusion multiplier value in Slic3r WITHOUT changing printer settings in memory?
Divide the amount overextruded by the desired amount. If you wanted 100mm but got 101mm, that's 1mm extra, or 1% over. Use an extrusion multiplier of 0.99 (1% under) to compensate - AND THEN DO ANOTHER TEST to confirm.

This modifier will be used by Slic3r to generate E values in your gcode without flashing anything. 

I recommend saving this recipe with an intuitive name, like Acme Green PLA.