The Wanted List feature of Bricklink is quite useful, but it is very difficult to use and does have some unfortunate limitations. Here's a quick-start guide to seeing which stores have the most parts you want.
1. Go to the "Wanted" tab, select "Parts", and click "Submit".
2. Choose the part you want including color, condition, and quantity.
3. Repeate for each part you're looking for.
4. Click the "By Shop" tab.
5. Select Sort By: "Lots (Unique)"
This will show you which store has the most items on your wanted list.
You can also search against your wanted list when you are in a store. After buying from a store, it is possible to remove purchased items from your Wanted List, but it does not happen automatically. The feature is a button on the "Orders Placed" page that I think is not even visible by default.
Give it all a try and see if you have any questions. Also, the people in the BrickLink forums are very helpful.