I know that I need to use Pheromones to make certain Throdama morph. My question is: Do I need use pheromone more than once on same female? What chance do I have to get morphed baby?

you can have a max of three throdamas using pheremones on the baby. the more pheremones, the stronger the morphs specific benefits are. Even if you use just one pheremone, you will still get a morphed baby.

i don't know what happens if you use a mix of pheremones but if you want a specific morph, it is best to use the same pheremone on the pregnant throdama.

You can't use a "mix" of pheromones. The menu let's you select only the desired morph. At least one worker must be assigned for the transformation to happen but the bonuses add up if more workers care for the mother and then the baby at once.