You can make a payment online even if you booked via phone. Well, at least I am able to.
Log into MDE. Under Disney Resort Hotel Reservations, there is a little line of blue font that says "View Details."
If you click on that, you can see your remaining balance and make a payment!
Same here. I booked a package (room + dining) over the phone on July 30th, and when I log in to MDE, I click on My Reservations and Tickets. It pulls up all my reservation details, which look like this (edited for security purposes):
"Disney's Port Orleans Resort - Riverside
Confirmation Number: ABCDEFG
Quick Service Dining
Check In: Day, Month, Year
Check Out: Day, Month, Year
Room Type: Disney's Port Orleans Resort - Riverside-Garden View
Guests: 2 Adults
Dining Plan:2015 Two Quick Service Meals per night
Remaining Balance: $1,234.56 USD
Make a Payment"
I highlighted the Make a Payment thing in
blue because that's how it appears in MDE, and I can click on that link to make a payment online.
I've heard that folks using Chrome or Firefox are having trouble pulling up their reservations to make online payments, so may want to switch browsers. I've also heard that RO reservations are having trouble paying online, too, so maybe because I booked a package, that's why I'm able to make payments online.