You'll need to use both device code sets.

Figure out which of the two code sets has the least number of commands you'll use. Program your receiver to that device code set first. Program all the advanced keys from that code set that you'll use.

Now program the receiver to the second device code. All of the advanced codes from the first set will remain on the keys where you programed them. Any new programming you do (with the second code set active) will learn those functions. Any keys which you did not program with advance codes will retain the default functions of the second device code.

—næstep