Most everyone doing planetary imaging will recommend that you use AS!3 for stacking. Then came AutoStakkert which is easier to learn and does a better job at stacking but that is all it does. RegiStax will do both the stacking and processing steps. In the beginning there was only RegiStax.
The stacking software will discard the low quality frames in your movie file and align the remaining images and more or less take the average of them. For stacking software there are two popular choices: RegiStax 6 and AutoStakkert!3 (aka AS!3).