Basically, you should have three maps: your first measurement,
your second measurement (note that you can use figure(number) to create new figure windows),
and your bias measurement.
Now you can have two bias-corrected images sc1 and sc2: (note that you can add ' ; ' at the end of commands to run the commands without printing the results!)
sc1 = s1.data - bias.data; sc2 = s2.data - bias.data;
These two together give you the final map:
sc = (sc1 + sc2)/2;
You can also calculate the variance:
diff = s1.data - s2.data; var = diff.*diff;
These two images will be used to determine the gain of your CCD.