SYSTEM OPTIONS => Configure Store layouts => your store.
On bottom there's the full list of products you can check so that they will be assigned to the store.
The important thing to understand is that you are not "moving" anything into the store: stores are mainly ways to allow different skins and checkout options for the very same products.
So, ALL of your products will always be part of your main store.
In general, the only thing you have to do to use a new store is altering your RTD link to use that, in the format:
designer.realtimedesigner.com/YourCompanyName/Storename/rtdlink.....
To be clear, this means that you can NOT setup products to be silent checkouts: that's a store property only, and so you determine how it will be via the link you provide your customers.
