If you pair one remote to your MacBook that will be the only remote able to control your MacBook. I do not believe that remote will be able to control anything else (not sure because I don’t have anything to test it with), so you should be able to use one remote for your MacBook and one for your dock.

Just try it. If it doesn’t work like you want you can always unpair the remote.

how do i pair a remote again?

Open System Preferences, go to Security, make sure you are in the General tab and click the Pair button near the bottom and it will tell you what to do.

I think it is incorrect, from experience, that pairing prevents the remote from being used on another piece of hardware.

Pairing, and allowing only the paired remote to be used on the Macbook, is a security measure used to stop others using their remotes when you’re sitting in a coffee shop to constantly put you into Front row, for example. However, the ‘use only paired remote’ restriction occurs on the Macbook, not the remote.

This means, unless your dock will also pair with a remote and only accept that for control (which I doubt), using the paired remote on the Macbook could in some cases (depending on hardware placement) trigger control signals being sent to the dock also.

Remote pairing allows for only that computer to work with that remote, but that remote can be used on any other computer.

For example, if you have computer A and B and remote Y and X, if you pair remote Y with computer A, remote Y wont work with computer A, but remote Y will still work with computer B.

To pair a remote to a computer, aim the remote close to the chosen computer and press and hold the MENU and Next/Fast forward button at the same time for about 5 seconds, a lock icon should appear on your computer screen.

it’s really weird. when i pair the remote with my computer it seems that now that is the only remote that will work with my computer or dock, and the other remote doesn’t work with either. is it possible that when i pair it with the computer, the infrared receiver on the dock is picking up the signal and pairing itself too?

There is a chance, but the reason you hold the remote close upto the computer is to stop other computers or docks from picking the signal up. Macbooks have the IR receiver on the front generally on the right. iMacs (aluminum ones) have it under the apple logo below the screen.