Depends on the merchant. I can't speak for B&N.
I know that Tupperware has some text on the confirmation page that says "MyPoints members click here to receive your reward" or something like that.
But I think when I've ordered from Lands' End, there was no such link and the points just showed up a month later.
Make a note of your purchase, and remember to check your account after 20 business days (that's the standard offer).
And SAVE YOUR CONFIRMATION EMAIL!!!!! At least until you get your points. If they don't credit after the specified time, you'll need it to claim your points.