Well first things first. You have to make a palette and get your images formated to use with mugen.
This video will show you how.
After that, make sure you put the palete in the same folder as the template and edit the def file so it shows your current palette file as the only one to use.
Then open the template and you'll notice all those black sprites, well you use those as a guide as to what groups to place your sprites in.
(they all have groups which you can see, like the icons are 9000's stance is group 0)
They are labed with a group number and a image number, the first frame of your stance would be 0,0
Make sure you add your images in on a shared palette if youve converted them like in the video.
After you have your stance sprites insterted you can open the animations from the icon at the top and go to the stance, there you can add the other frames in and edit the speed.
You may want to look up a video on youtube that shows you how to further use fighter factory.
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