"Goodbye" is always polite and always friendly. Don't feel you need to use anything else.
In English, we often use the word "see" figuratively to mean "meet" or "have social contact with." I never even thought about how strange it is to use in a telephone conversation. There are other such peculiarities.
As for whether to use "see you," a native English speaker picks up cues from the other speaker and matches their level of formality and their turns of phrase. In closing a conversation, it is common to echo what the other speaker says.
English speakers use many different phrases to close a telephone conversation. Any phrase that can be used in person is also used on the phone. "Bye," "Bye-bye," "So long," "See you," a few friends of mine even say "Ciao."