We only make our reservations online. Instant feedback as far your confirmation number, nights reserved, deposit/balance due status, etc. Then Disney follows-up with an email confirmation.
Last week was the first time I've ever phoned Disney to make sure my reservations were still in their system. I did this based on a couple of postings here about people's reservations disappearing. Mine were fine. To date, I've never had a problem with the online system or having a site reserved when I arrived at the welcome center.