Never forget: Your customers are likely to use the different sales channels you offer in different ways. Some of your customers may buy exclusively over the web but visit your brick-and-mortar stores to see, feel, even sniff your products (or, I suppose, your personnel) before they go home to order. Customers may, say, visit the Orvis store once a year, but always place their Orvis orders online.*
If your physical stores are taking on this role of sampling locations where a customer makes a tactile connection with your products (and brand) for later purchases on your website, it's not necessarily a negative.
However, it does need to be planned for. It can be sabotaged quickly, for example, by overly aggressive onsite salespeople, or it can be enhanced by discount- or QR codes (If you're not up on your alphabet soup: QR codes are those two-dimensional barcodes that take you, via scanner, directly to a specific website) that let web or mobile purchases track back to store visits.
This may seem like an obvious insight, but its implications extend to how you design your compensation systems, and, frankly, to the tenor of the conversations you should be having with your people who work in various channels. Has the "sales staff" at your physical location now become essentially a sampling team providing advance work for sales you will later make via the Web or mobile devices? If so, offering commission based on aggressive sales targets - and lambasting your personnel when they fail to "make their numbers" - is not going to serve your company, or the customers your employees ultimately take their frustrations out, very well.