It may seem that separating products available for immediate purchase online from the products available only in brick-and-mortar stores makes sense. You may even consider listing all products together and then make the store area separate. The problem with either of these approaches is that you repeat product descriptions and increase the path to the checkout, which will reduce your online sales.
Take a look at what Toshiba is doing on their site:
At the first glance, it seems the content in Research section is focused on showcasing the benefits of Toshiba laptops and is a marketing tool designed to increase the desirability of the product. However, on close inspection you can see that the content is duplicated in Toshiba Direct, the online store: overview pages for Satellite L730 in Research and in the store. Yet, the pointlessness of such a setup is even more obvious when looking at the model listing matrix: in Research calls to action are weaker and are likely to result in fewer conversions than the calls to action in the store. (I just wish I had the actual numbers but given such a separation I don't think Toshiba even tracks performance here.)
Instead, you should have just one list of products that clearly indicates what can be purchased online right away and what can be found only in physical stores. The techniques to accomplish this are plentiful and you can test any of them to see which one fits your layout and pleases your users the most.
In the product list, you can show store exclusivity as simply as indicating the item isn't available for delivery, like Fry's Electronics does:
or if you have the
Add to cart button in the product list simply replace it with the button
Find a store /
In Store Only like Best Buy does:
The same technique will apply to product pages. However, you can go a bit further let visitors search for a local physical store (if available) straight from the product page without additional clicks to reveal it, like Toshiba does in the Research section of their site:
You can also give visitors the option to filter out items based on their availability like the already-mentioned Best Buy does in their left-side filter section: