iSync has absolutely nothing to do with storage devices. It has to do with synchronizing address book-type data between your Mac and any one of a number of handheld devices (PDAs, Cell Phones, etc.)
"Syncing" your data between the internal HDD of your Mac and your new external HDD is more of a concept than anything else. If you're looking for automation, your best bet is to get a data backup program. Retrospect from Dantz is an established program which you can use to do this; however it's commercial and not exactly dirt cheap (although you do get what you pay for).
Another alternative is Mike Bombich's Carbon Copy Cloner, which will basically make a duplicate copy of one drive onto another, and also has a range of useful features.
Naturally, the absolute cheapest option available to you is to simply drag-copy all of your user data to the hard drive yourself, and then on some kind of periodic basis copy over new or recently-changed data. It isn't automatic, and of course requires that you actually do the keeping-track-of and copying, but it's the tried-and-true method that most people out there (including myself) use.