If you have pollen from the same strain you plan to pollenate it's not cross breeding.
If you plan to use pollen from a female auto that you are herming for fem pollen,
all the seeds produced will be mixed phenotypes. your first generation of seeds, F1, will not show any auto traits at all...
If you are using the TM for the fem pollen you will have to use it again on one of the females you grow with the F1 seeds
Again for F2
and F3
and so on until you get 100% autoflowering hybrids in the F5 generation. You will again need to do it for an F6 in hopes of stablizing the strain.
The Spyder auto i have now is F9. and it took him till F8 to get the genetics stable enough for marketing.