Ja(jaa) means like "then". "Mata" means see you. So it could be "see you then" or "then, see you!" "Ne" is used to make a sentence sounds softer. eg: きょう は てんき が いいです。 きょう は てんき が いいですね。 You can say only "mata!" as well but adding "ne" sounds like more friendly.

They mean the same. We use them colloquially. We also say: Jaa mata, Ja matane, Jaa matane, Jaane, Dewa mata...etc. They mean the same like "see you" or "bye". ("Dewa" sounds more formal than "ja" or "jaa".) I hope this helped you.

jaa matane = then see you or then bye matane= see you next time, ok ? /see you ok?..