I, too, have my data on a separate partition. Actually, I have identical copies of all data on three separate partitions that are on three separate drives, with one of those drives being an external drive that I sync once a month with the other two. When I installed Mint, I just left all data where it was. I simply created a partition for Mint and installed it (I dual boot with XP). Mint reads and writes to ntfs partitions just fine, so you'll be able to access your existing data from Mint.
When updating Mint I prefer a clean install (plus I like to tinker and have the time), so I always start from scratch. As I learn how to do things I write directions in a big text file so that when I reinstall I can just go through that list without needing to remember how I did various things. I find that redoing everything with a clean reinstall helps me become more comfortable with Linux. It's probably not a bad idea to keep your home directory (where most of your settings are) on a separate partition in case your system gets hosed (I don't, but I probably should). And many have a third partition for swap (I don't, and my system works just fine).
Linux Mint 17 Mate, 16GB RAM, 64 bit Intel CPU