All you should have to do to use a name of your own choosing is type it into the blank space provided when you select "new career."
Hitting the RN button to generate a random name for your kaleun will use Commander's database of "real" names to create one for you, but you don't have to do that nor do you have to add your desired name to Commander's files. Just type it in is all.
I know because I started a career as Rufus T. Firefly once.