It is better to put those settings in user.config so they don't get lost during upgrades. If you make changes to user.config you have to touch Web.config to make it see your changes.
If you added them to Web.config note that they already exist there and if settings are duplicated the ones lower in the file take precedence. So for example if it has
<add key="Site1-PaymentGatewayUseTestMode" value="true" />
further down in the file then it won't show the checkout because you have only production settings. You need to put it in user.config and make it false.
Also if you have a multi site installation you should make sure the SiteID is 1 or else change the prefix Site1- to match your actual site id.
WebStore is a very basic feature at this point. It does not currently have support for products where the user picks the price.
Hope it helps,