So I selected the native segwit account to send BTC. When it went through It ended up in the Legacy account and not the Native Segwit Acccount. What the heck?
No doubt you did something wrong, because you should see all your accounts (Legacy&Segwit) if you created them correctly. I think you missed doing some steps, probably to add new account. I will post you link to nice tutorial so you can check step by step what you do wrong.
https://atomic.loans/blog/native-segwit-on-ledger/