I think you actually "exchange" the funds from the traditional IRA into the Roth. It's not super straightforward on their website, but I've always found their phone reps very helpful.
It's never taken me more than 3 minutes on the website without calling them. Pretty sure you log in to the Roth account and then choose your contribution and when it asks where the money comes from you choose that you will fund it from the money you already put in the traditional IRA, I guess by exchanging it. Pretty simple IMHO, though I will say the Vanguard website itself is kinda clunky in regards to user interface.