ecommerce a channel or a segment

How would you position ecommerce in a multi-channel company selling to customers (both b2b and b2c) from their web-site and through one or more of the channels (retail stores, sales teams, telemarketing, resellers etc)? So, far I have known several companies where I found internal conflicts to the extent that it signifcantly hurts the sales, brand and customer satisfaction.

Why does is happen and what to do about it? What is the right way to think about it, and who has done it best? More later.