How do I prepare fresh clams for clam chowder?
Cook them first. I consulted few recipes including this very representative 5 star recipe from Anne Burrell, she uses one dozen little neck or cherry stone clams per serving.

Scrub the clams and put them over high heat with one cup of water, covered, for 6-7 minutes. Remove open clams (careful, don't waste any juice). Continue cooking unopened clams for another 2-3 minutes. Toss clams that haven't opened.  Remove shells and coarsely chop meat, again, careful with the juice. Strain the clam juice from the clams themselves and from the pan through a coffee filter.

The clams are added to the soup as the very last step, so you won't overcook them this way.

As always with a Food Network recipe, it's worthwhile to read the reviews, but take them with a grain of salt. Some people are idiots. Have fun!