The new version of registax (currently beta, which I don't have
) will allow you to align on multiple points at once.. registax will then go through and align on those multiple points and blend them together at the stacking stage.
But in my case, it's simply manual MAP (multiple alignment point) processing. I ran through registax aligned on one feature, saved the image, opened the avi again and ran through aligned on a different feature, saved that image.
I took them into photoshop and copied one image on top of the other as a layer, lined them up, and deleted the blurry parts to show the sharp parts from the layer beneath.
It's becoming a common way of processing lunar images because of the scale of them, and the "wavey" type of seeing you get where in a single frame you can have one part of the image sharp but the other part not sharp. This way you align on multiple areas which will end up with the sharpest image of THAT area.
You then just need to join them all together in photoshop.
It'll be much better when registax can do it by default, as long as it does it well.