Seeing as their web prices are the same as the shop, you'd hope that to get people to come into their shops to buy a book, rather than wait for it to arrive by post, their "Check local store" type search would be up to date? Sadly not.
So my usual process for buying a book goes something like this:
Find book I fancy - see if Waterstones have it locally so you can have a quick look - go to store if it says they have it - find they don't - check Amazon and find its a good few £s cheaper - order from Amazon.
If the shop price was a couple of quid more than Amazon, you'd often buy from the shop to get instant gratification, but when its more often than not half the shop or Waterstones web price, its a no brainer.
As for e-book prices, forget it, still cheaper to buy the paperback most of the time and its still easier in physical format for technical books and non-fiction with colour photos.