If you're talking about the nraas mod then I can give you some steps to try.
- Click on the mare and select Master Controller
- It should bring up a list of options but you want to click "Basic" which should be somewhere towards the top of the list
- It should show up another list and you want to select "Pollinate"
- If you're breeding with a stallion in your own family household then click "active household"
- It should bring up your horses and you can just choose whichever stallion to breed to and submit it
Hopefully this makes sense?