Post-Processing:
I use DeepSkyStacker to align/stack my lights as well as to subtract my dark/flat frames. Here are my steps in doing it. First, open DeepSkyStacker (DSS). I'm going to refer to v3.0.6 as that is my current version. On the left hand side, click Open picture files. Locate your Light frames. Do this with dark files and flat files.
Click Check All on the left hand side. This will place a "tick" on all your selected files. Now click Stack Checked Pictures on the left hand side.
This will bring you to the Stacking Parameters menu. I normally leave everything set as default, however, you can try other methods which ever way will give you different results. Click Ok when done.
DeepSkyStacker will now do its job stacking your selected light frames as well as subtracting your dark/flat frames. Will take 5-10 minutes depending on the number of files you have selected as well your computer specifications.
Once this is done, click Save Picture To File. Ensure you place a "dot" on Embed adjustments in the saved image but do not apply them. Select the location you want to save the file to and your done.