I can only echo Brett's thought that you need to check with the state where your kids will be born.
My kid was born in Florida, long before I transitioned. I haven't pushed hard to get them to do anything, but they have not been particularly friendly or understanding when I've tried to ask questions about it. As it stands, I can't in most situations prove that I am the parent of my child unless I produce the original unaltered birth certificate along with my Oregon name change court order and current state identification, and even with a pile of documents people don't always believe me.
I know it's stupid, but just making sure you have the same last name as your children can make a big difference. After I changed my surname, or when I used my daughter's surname in practice before I had a court order, I was almost never asked any questions at all.
Also I want to point out that reality and facts and rules aren't necessarily relevant with the formation of birth certificates, but once they are written they are generally treated as carved in stone, towering edifices of information. It can be difficult to change them if you need to later, and even if you do, any court that needs to examine any details about you or your family will likely treat the oldest documents as the most valid.
I just realized all this only applies to the U.S. I have no clue what you might be facing if you live elsewhere.
