iOS 6 combines your phone number with your Apple ID email address, which makes it possible for others to iMessage your phone number and have those Messages sync across your devices. Whereas, previously, with iOS 5, one had to use Apple ID email addresses only in order for it to sync across devices.
First, you need to make sure all your devices are on the same Apple ID.
On each iOS device (iPhone, iPod Touch, iPad, iPad Mini):
- Open Settings.app
- Go to "Messages" and make sure iMessage is On.
- If iMessage is on, "Send & Receive" will appear below it. Tap on it.
- Make note of the Apple ID at the top of the page.
- Select your phone number and email address(es) that you want to sync to that device.
On each Mountain Lion Mac:
- Open Messages
- Click the "Accounts" tab in the top.
- Select your iMessage/Apple ID account, and make sure "Enable this account" is checked.
- Select your phone number and any email address(es) that you would like synced.
The most important part is that everything is consistent across all the devices.
Note that only new iMessages will sync - history will not.
If you are still having trouble getting new iMessages to sync across the devices try:
- Disabling then re-enabling iMessage on each device that isn't being synced to.
- Delete all your previous conversations: Some people have reported that they had to delete all of their conversations before things would sync up.
- Make sure you have your phone number added to your Apple ID account online.