Depending on the Quicken version you are running, it may or may not be compatible with OS X Mountain Lion, the Mac OS X version included in the Late 2012 iMac.
Quicken 2007 (Lion version) and newer versions are compatible with OS X Mountain Lion. If you have an older version, you will have to purchase the lastest version
Quicken for Mac is really awful. Sorry to be so blunt, but it does. Go to the Intuit/Quicken site and do a few minutes of research. You will see literally hundreds of really harsh criticisms, and no solutions. It is so bad, I used Parallels on my Mac, so I could load Windows and then use the PC version of Quicken, which is really great.
Nowadays I use iBank as my banking software. It is designed for the Mac and works well. And they are constantly improving the product.
Hope this helps.