1) Hit the Select Input button and open the .avi video or set of FITs files you wish to process.
2) Make sure the Colour processing box is checked and I like to also check the LRGB option but it's not required.
3) You want to use the best frame you can find for the alignment reference. You can drag this slider at the bottom and view the frames as they change or just select the slider and use the right and left arrow keys on the keyboard to move through the frames until you find one of the best frames.
3a) Select an alignment box that will fit around the planet, center the box over the planet and then click the mouse. The program will automatically switch over to the Aligning tab. Alternatively, some imagers like to use a smaller box and center it around a feature like the southern polar cap. When processing images of the moon I usually use a small alignment box and a feature like a crater to perform the alignment.