I ride every day in Toronto (which is fairly different than boston however) and parking isn't an issue usually - lots of places to tuck a moped behind dumpsters, behind barriers, etc. (Helps having a vehicle you can pick up and lift over things) As for security, a good lock will be a start - generally I go with two theories when finding a spot to put it... either maximumize the amount of people who see it, or minimize. In other words make it almost impossible for people to stumble across it (out of sight, out of mind) so they don't mess with it or if you can't do it, put it in the most public place possible so anyone trying to do things to it will (hopefully) get discouraged by the amount of people able to see what they are up to.
Ideally however you'd have a place to lock it up which is a little out of the way (Mine I keep inside a fenced courtyard outside my building and I haven't had an issue, mostly I suspect because it isn't visible at all from the street)
Main things with city traffic is to keep your eyes open ALL the time for what other drivers are doing (they will fail to see you, even when you think you are bloody obviously there and SHOULD be bloody obvious), keep an eye out for people pulling stunts like unsignalled turns, lane changed. Sudden unsignalled and illegal u-turns in front of you, pulling out from alleyways, passing FAR too closely to you (you have to keep peeking into your rear view mirrors to have an idea of whats behind you) Main thing is be aware of whats going on, because you can't rely on cagers to do the same.