We did this on a recent trip. Bought our Citypass online and picked it up at Will-Call at the
Disneyland Ticket booths. For our trip, it worked out that we visited SeaWorld and Universal before we started the "Disney" part of our trip. All in all it worked out good for us. We did get a 265 credit toward the purchase of the new tickets. We ended up adding one day and it was 24.00 per person.
The ticket agent did ask us if we had used the ticket already for Universal and SeaWorld and we had. They did let us keep the Citypass tickets, so we could keep them as a Souvenir. Disney gave us new (paper) park hopper passes with the extra day on them. All in all, it was pretty simple. I wasn't sure why they asked us if we had used the SeaWorld/Universal tickets first, maybe because they would have had to things differently, but I didn't ask since we had.
The only small snafu we had was we originally tried to upgrade the tickets at the front desk concierge at the Disneyland Hotel. I had called from our room and talked to someone and they said we could upgrade Citypass in the Hotel. I had thought that I would save time in line at the Disneyland ticket window. However, when we went down to the lobby, the cast member looked at the tickets and said she'd never done that before so she talked to a "supervisor" who said "since they were "discounted" tickets they couldn't be upgraded at all." Luckily I had done my research here on this site and on CityPass's site and knew that was false. I told the cast member it was not true either and had her look it up on CityPass's website. She was surprised but said that it may only work at the ticket counters, which it did. Luckily, I knew better and didn't just listen to the castmember when she said they couldn't be upgraded at all.
Overall the Citypass tickets were great. I got to experience 6 days in 4 different theme parks (with the 1 day added at Disneyland) at a pretty reasonable price.