You have to look for your item in several stores, and of course don't hesitate to ask to vendors. Even in big stores you can find great deals (particulary if they have a "used stuff" floor).
To give you an example, i found a Shin Musha Gundam from Gundam Fix Figuration toy line at 1900JPY instead of 4000JPY.
Best advice is: take your time, look everywhere, you will eventually find what you want at a good price.