Okay, so I know that your supposed to do the pheromones to get different morphs, and I bred two that was *supposed* to get me a defender, and then I heard your supposed o assign a male to a female? How does that work??

You can assign 1-3 throdama with ready pheremones to a pregnant female. These throdama can be male or female, it doesn't matter. The more you assign, the more special abilities the baby will get. (You can't assign two different types of pheremones, though--they have to all be Defender pheremones, or Scouts, or whatever.) 

No- I mean HOW do you assign them, where do you go to do that? And do you do it while the female is pregnant, before you breed her, or after she has given birth?

You assign them while she is pregnant. There is a menue that will appear and allow you to choose between warrior/defender/scout/harvester, and to assign bugs that have those pheremones ready. 

I can't figure out how to embed an image, but hopefully this link will work. 

https://imgur.com/oVimAdy

See "Use Pheremones" at bottom left? That's what you need to use. 

You can't assign the mother to her own baby, and you can't assign a throdama that is busy with anything--they have to be active, and assigning them will keep them busy until the baby grows up.