My experience has been pretty good. I get iMessage notifications on my Mac desktop, Mac Air, and on my iPhone. If I read a message on one of my Macs, the notification is cleared on my iPhone. Same experience if I read it on my iPhone first; it clears the notification on my Macs.
The only issue I have seen is if the notifications come to my device after I have read it on the other device. For instance, if my MBA is "sleeping" and I receive iMessages and read them on my iPhone. In this case, I receive the queued up iMessage on my MBA when I "wake" it up.
You need to set your caller ID as your Apple ID that you are using on your phone, instead of your phone number.
Otherwise, it doesn't know where to respond to. iOS 6 GM will bring full merging of iPhone Number and Apple ID, so that it will pair them in the future, but I don't think it works properly as of yet, so use the iOS method I posted in the first sentence.
Thank you. I will have to wait for the "merging". That really answered my dilemma.