In this document i will give you a couple of choices to make with reguard to sizing and such, my preferred method is all ways in emphasised text. I will also be assuming you are pretty competent with the program.
Route 1:
In order to stack images in Photoshop each image must be exactly the same size. The
one way to accomplish this is to choose a star near to the upper left of the
subject in each image to be stacked (use the same star in each image). Using the
crop tool, click on the chosen star (zoom in for greater precision) on the first
image and drag the tool to a place close to the bottom right of the subject. The
Info window will count the number pixels in both the x and y directions as you drag
the crop tool across the image. Note the pixel count in the Info window and use
this value to crop the other images that you want to stack. By starting the crop
each time on the same star and ending with the same pixel count, each image should
be the same area and size.
Route 2:
First use the select tool to select a box of the required size on a single image,
once done create a new image with a transparent background and the same dimensions
as the original (not the selection). Once the new blank image is created and copy
/ paste the selection into the new blank canvas, the select the background and inverse
that selection(CTRL+I). You now have a full sized image with a single selection inside.
One image at a time copy/cut and paste the other images to be stacked into the template
image, doing a cut and paste of the selected are into a new image. After several
iterations of this process you will have a bunch of images that are all the same
size and area as each other.
After you have scanned, cropped and saved your images. Reopen them in Photoshop. With one of the images you will need to create a layer. To do this, select one of the images, Create a new layer(SHIFT+CTRL+N) and while it is still active, select the other image, copy and paste it to the previous image's active layer. Using Difference as a blending method for the top layer will make it easy to see when the layers are aligned. You will get a totally black screen when exact alignment is achieved.
Use the arrow keys to register the top layer with the bottom, some people suggest rotating images but i tend not to do that. I would rather concentrate on the subject and ensure that it is aligned perfectly. Some images will be harder to align than others, some will be easy. Keep going using the bottom layer as a reference every time and you will find you have a stack of perfectly aligned images. You can use the eye button on the layers palette to hide any layers that are completed. If you have severe field rotation at the edges of your exposures you MUST concentrate on the main subject of your picture. Don't worry too much about the edges of the images just get the main subject registered.
Now your images are all registers you can begin the stacking process. The first method was developed by Jerry Lodriguss. The second is of my own cooking. Again my preferred method is emphasised.
Route 1:
After the images are registered, go to the Layers Palette, and change the method
that they are combined to Multiply / Overlay [from Difference].
Then Flatten the image to combine the two layers (flatten command is under the small
right pointing arrow at the top right of the layers palette).
Route 2:
Although this method is a bit long-winded i think it gives better results than the
above method, again the choice is yours. You wont know unless you try both methods.
With this method the registered layer is copied to a new file and saved as a copy
in the tiff or psd format. The original layer can then be deleted.
What you have now are three images, the two originals plus a registered version of one
of the originals. The original image can now be closed. At this point you will Add the
registered image to the remaining original using the Apply Image function found under
the Image menu. Note that Opacity should be set to 100%.
Thats it for aligning and stacking the images, you can read a little document about masking by following the link below but this can be quite a fiddley job to do and if you can get relatively good results with the above methods it is not really worth the extra aggravation. Masking Images