We never had a Welcome Home Trip, so my response isn't based on that detail. But we've always found either approach gets you the same result when making reservations. Online tends to be much faster. I only call MS anymore if I might have a specific question or I'm someplace I can't get online.
I'd recommend you get online, log into your DVC member account, and do a little 'playing' for research to see how it works. Also, just a tip (that you might already know). Whenever you make a DVC reservation, you'll get a confirmation number. You'll need to manually link that room reservation with the confirmation number to your My Disney Experience App - that won't happen automatically. So don't panic if you make a reservation and you don't see it in your app - just link it once and you're good. Another tip - don't worry about adding every single guest you're expecting to be included on a particular reservation while making it. If you are the primary, make sure your info in correct. After you make the reservation, you can more casually go back in and modify the guest list on the reservation. Welcome home!