I asked Mitch from Mephisto Genetics about this very topic (photo pollen on femal auto/auto pollen on female photo) and in a simplified nutshell he said that it doesn't really make any difference. Pick the traits you are looking to pass on and breed with those. By the time you work a non auto to auto you will have worked through four generations of selecting for the traits you want passed on. Then end result will give you no inclination as to whether the photo parent was a male or female, or whether the auto parent was a male or female. That's what I got from it at least.
As long as one of the parents is an autoflower than the genetic trait will be passed along to the offspring. They won't show up in the first generation, but the second generation should have 25% autoflowers for you to select and breed together to create more autoflowering seeds. From those you can pick and choose what you like to further stabilize the more specific traits you're after.
If I'm off on any of this someone should chime in.
@gbd thx for that info m8 very much apreciated but can you also tell me if i have to use auto pollen again for 2nd generation cause as you stated there werent gonna be autos first run so how will i know what phenos to use for 2nd gen if you know what i mean
hope you can tell me m8