There are a lot of Threads on this, and I'm sorry if this is just redundant. But this worked for me and wanted to post these two links together for anyone trying to do this. Most of what I found was extra, unnecessary steps. Hope this is helpful.
This worked perfectly for my Logitech Harmony
1 - Controlling two TiVo boxes with separate remotes
2 - Then, Do what this says
Now I have 2 Premieres, 1 remote. Controlled completely separate.