How to swap function of Caps Lock and Control keys with external Mac keyboard?

KeyRemap4MacBook (soon to be renamed “Karabiner”) can do it. You’ll need to create a custom item in the xml file, and you can specify the device that it works on.

If you need even lower-level control over keyboard, you can try Seil (formerly “PCKeyboardHack”) from the same author.

I’ve been using both for a few months, and they are great. I customized several different parts of my keyboard:

• I set my caps lock key to act as escape when I tap it, and as control when I hold it, so those are easy to reach.
• Then I made my control key acts as ctrl-opt-cmd so I can easily perform custom shortcuts I make (either in Syst Prefs or BTT).
• I set my esc key to toggle caps lock, so it’s far out of the way.
• I made my left shift key be an opening parentheses “(” when I tap it, and shift when I hold it.
• Similarly, my right shift key is “)” when tapped and shift when held.

Plus a few other minor changes.

If you want a hand setting up the custom xml item you’ll need, let me know. The documentation is fairly sparse, and most of what I know about it I learned from looking at the built-in example settings.

 

From your screen shot of the keyboard prefs - click on the Modifier Keys button.
You should see a drop down (Select keyboard: ) that allows you to change the modifier keys for any keyboard that's attached to your system.
But, you WON'T see that choice unless you actually have another keyboard attached to your MacBook Pro.

And, that's to allow you to do what you want, have a different modifier key configuration used on separate keyboards. Then, your Mac will know which keyboard you are using, and will use the correct settings for each, on the fly. Works great. and no need for other software to do that.
If you need to do something other than only switch the modifier keys, then you'll need another solution, like Qaanol suggested.