If you are Stacking as opposed to Average and Sharpening your Frames, and your lighting is not constant, then you may need to use Balance Colour and Brightness. It is on the Stack menu. There are two versions of this function the Global one is quick and is sufficient in most cases. The Local one can produce superior results if the lighting is patchy and varies between Frames. This is a much slower function and destroys any filter that was already there. It can also produce artifacts, so you may need to be careful which frame you make active before starting. Both functions now start with the Active Frame and try to balance the others to this.
Before Frames can be Stacked or Averaged properly, they must line up with each other so that the same features in each coincide. If this is not done you will get multiple edges from different Frames in your finished Picture. CombineZ offers several solutions to this problem. All of the menu items mentioned below are on the Stack menu on the Size and Alignment submenu.
You can move an individual Frame about relative to its neighbours by making it visible and then holding down Shift or putting Shift Lock on and pressing the arrow keys. This rolls pixels off of one edge and onto the opposite, so you can roll them back if you go too far. When you are satisfied, use the Tidy Edges menu command to make the edges less unsightly. After this operation the Clean Rectangle calculations may be incorrect. Hint: use the mouse pointer to mark a spot on one Frame, switch to another Frame, and using the arrow keys, bring the same spot under the mouse pointer again. If you use Caps Lock remember to turn it off when you finish.
By far the easiest way to align frames is to use one of the Automatic functions. All Frames are aligned with the Active Frame. The Single Pass version is faster but less accurate than the Two Pass one. Use the Single Pass function if your Frames vary wildly in size and alignment. The Two Pass function resizes all Frames by the average step between Frames and then on the second pass moves the frames and does any minor size adjustments that are necessary, thus it works better if the Frames were taken at regular intervals. The Active Frame is not altered but the rest are brought into alignment with it.
If you can establish a constant resizing factor, perhaps by observation of the Progress window, or by some other means such as trial and error, then you can use Resize All and enter this value. You may get superior results this way.
The most powerful method is to use Resize/Rotate/Move which brings up a box bristling with parameters. Fortunately there is a fairly easy way to set these parameters by using Points. The idea is to set Points 1 and 2 on one frame and Points 3 and 4 on another, then click on Set and Use Parameters on the Points dialog. This causes Resize/Rotate/Move to spring into action and adjust the size, orientation, and scale of the frame containing points 3 and 4 so that points 3 and 4 fall on top of points 1 and 2. So just select two widely separated points that are visible on two frames and set points 1 and 3, and 2 and 4, to corresponding points in both frames, and away you go.