You can't leave them in a couple of bottles to ferment out, because you'll get bottle bombs, just as you would if you bottled beer before it was done fermenting.
Here's three ideas or methods you could use:
1. Make some of EdWort's Apfelwein, a dry, wine-like cider. You'll find the info in the wine forum, I think
2. use the method in www.makinghardcider.com
- a semi-dry, sparkling, bottle carbonated cider using a method where you let the cider ferment out, add flavoring and backsweeten with a none-fermentable
3. I make a simple draft-style cider using a stove-top pasteurizing method - http://www.singingboysbrewing.com/Apple-Cider.html
and there's a sticky thread about it in the cider forum