Even easier way to tell: Manual has 3 pedals including clutch. SMG II has only 2 pedals like an automatic, since the computer and hydraulics operates the clutch for you.
I would recommend setting aside $2000 per year for maintenance related costs. The trick with an M3, or any BMW for that matter is to stay on top of maintenance so you don't have as many repairs. A repair is likely to cost you a lot more than if you kept the car properly maintained.
You'll want to get a copy of the maintenance schedule for your model-year. It will spell out what needs to be done at every oil change, Inspection I and Inspection II. Plus there are a few things you do based on time, not mileage such as brake fluid flushes.
If you really want to maintain the car in the best possible way, to ensure a long life with fewer problems, get a copy of the lifetime maintenance schedule from Mike Miller in the BMW CCA. His schedule and advice takes the standard schedule and does a few things more often, and adds a couple things missing from the schedule which should maximize the performance and lifespan of your car.
I bought my 2002 M3 just over 4 years ago when it had ~45,000 miles on it. It was an abused and neglected car, which I probably shouldn't have bought in the first place. Luckily, an aftermarket warranty saved my ass when I had to do several thousand dollars worth of work in the first 2 months of ownership. However, since then, I've gotten all the maintenance in-line and up to date, and I haven't had any other problems with the car. I use it as a weekend fun car, and put less than 5,000 miles per year on it. But I intend to keep it pretty much forever, or until the day I finally get my dream car: an Aston Martin.
BTW, for my low-mileage car, I do an oil change every year regardless of the miles. I also do the brake fluid every other year, though I am considering shortening that to every 12-18 months. Everything else I do according to Mike Miller's enhanced maintenance schedule, which I started following this year as I ticked over 60,000 miles on the car.