Hello there. You may have already found a solution for this, but if not, here is one method for doing this.
You must first "un-pair" the magic remote from the TV. This is done by pressing the Back and Home buttons at the same time for about 5-10 seconds (you'll know it's unpaired because the arrow will disappear and doesn't reappear when you shake the remote). Un-pairing the remote and TV apparently disables (?) the RF signal function from the remote control and allows a "learning" (universal) remote to access/read/process (?) the magic remotes IR signals. (someone stop me if I'm talking out of my ass...)
After the magic remote is un-paired, just follow the universal (dish network) remote's instructions on how to learn commands/signals from another remote (the magic remote). Once the universal remote is setup and working, you can actually re-pair the magic remote with the TV (done my pressing the OK/scroll wheel button), thus allowing you to use both remotes on the TV, if need be . . . and unfortunately, it need be (read on).
There is one caveat to this, and it's pretty major . . . unfortunately, since the OK/scroll wheel button is used to re-pair the magic remote to the TV, every time you use/press the equivalent "OK" button on the universal remote the TV thinks you're trying to re-pair a magic remote and tries to register (pair) that remote. This of course fails, and subsequently, the OK/Enter command fails. So, in essence, you can navigate throughout the TV's menus and Home screen with the universal remote,say, to the Netflix app, but as soon as you press OK/Enter to open Netflix, the TV tries registering the remote. Kind of a huge bummer...really defeats the purpose. (sorry if I just wasted your time!)
If any other community member(s) knows a fix/work-around for this, please share. It would be greatly appreciated.
Anyway, hope at least part of this helped you!