Hi Mrhoni!
That is the reason I installed the second Hopper in our master bedroom! However when the installers came they said I could have BOTH installed in our dedicated Home Theater Room and said each of their IR Hopper remotes have different codes and if they didn't one Hopper remote would control the other in a different room! Since I had already had all the inside coax wiring done, per-installed I didn't want to change anything on the initial install.
We started out using our new factory DISH Hopper remote, to control the Hopper, TV and A/V receiver as we had in the past that was also controlling our DirecTV DVR (we had both before canceling DTV with this install) as well as our previous DISH VIP 622 DVR. Since the factory Hopper remote is not back-lighted we both had problems using it, and had to put the HT side lights on dim.
I went in to modify our Harmony One remote "On-Line" and removed the DTV set up, and removed only the VIP 622 DVR under "Watch DISH" and entered Dish Hopper and their program excepted that and to my surprise it worked! Under the set-up of DVR Hopper it asked for a code that I did not enter any number. I suspect that you can have a set-up for DISH Hopper #1 and Dish Hopper #2 using an entered code. I recommend that you contact Logitech "On-Line" or phone to resolve your issue, if you want to use your lighted Harmony remote to control both. I believe that it is doable. Also when you resolve this, please post what is need to perform this so others will know, too. I did not find any previous post on this subject, but I did find one that said you could not have two Hoppers in the same room, that I now know is not correct. Good Luck!
