I have zero real experience with autos but here's the theory as I've gathered to at least get you going in the right direction to look into further if you want:
There are two real methods to breeding:
Pedigree method where the plants with the best traits are kept for breeding and plants that have undesirable traits are removed from breeding. With the goal of ending up with the ideal plant (whatever that is to you).
And backcrossing method where you start with a mom that you want to improve on in some way (in your case your mom would be a photoperiod plant you like and the trait you want to bring in is autoflowering). You do this by finding any single trait you like in another plant and would like to add into your mom's genetics. The plant that has that single trait can be complete crap outside of that one trait - all you are really concerned about is that one favorable trait ... all the other genetics of that plant are going to be removed by the following method (in your case you just need a plant with the autoflowering trait):
Take the seeds from the first crossing (photo per. mom X auto f. plant). Grow out the seeds to find out if any of them autoflower. If any of them do, take your favorite, and then cross it back to your original photo per. mom. Take these seeds (which are now only have 50% of the autos genetics) and grow them out. You should have a greater percentage turn out to be autoflowering. Once again, take and cross your favorite back to the original photo mom. Take these seeds (which are now only 25% of the autos genetics) and grow them out. Continue this process until the trait is stabilized in almost all offspring (99+%) and the genetics from the auto plant will otherwise be gone (except for the one autoflowering trait you've kept backcrossing). After 6 or 7 backcrossings you should be there.
There's way more to it in details, but it would take a book to put them out there. Hope that helps though.