I went through the same hassle a few years ago when I needed an mmsi number for my new epirb and ais radio. To further complicate things I am a licensed ham radio operator so I already have a lifelong assigned cal sign that I have been using for the last ten years and know as well as my first name, and there was no where in the forms to put down my existing call sign so that the new license could be associated with my existing call sign. So I now have two call signs to try and remember which to use for what. Its not a huge deal but would have been nice to use just the one I know by heart. One more first world problem I guess.
Hmm... I did it the other way around, but I thought there was a space to list existing call signs. Anyhow, since Marine Radio and Amateur Radio are different "services" they naturally have different call signs. Although it does seem odd, since you can switch between "services" just by punching a button on your SSB set.
Since I live in a very small town, it was interesting to look up the FCC license database for people in my zip code. Half of all the licenses are held by one guy, who lives a mile up the road from me and has a very obvious antenna farm going on. There are a few people with curious licenses for stuff that I don't recognize, but appears to be for some kind of remotely operated equipment. I am the only person in town with a marine radio license. I guess most people just don't bother.