Hello and sorry you're having problems. Offhand, you're not going to be able to use the Samsung remote (this is the same for most all TV manufacturers as well) to change channels since the channel changing occurs within the Charter box. The native TV remote can't be programmed to operate a cable box. The best you can do is get "basic" functionality of the TV using the Charter remote (On/Off, Volume and Input). However this won't help with the Samsung speakers, and you would still need to use a second remote for that.
What I would propose- and this is what I setup for ALL of my clients (as I am a Home Theater/AV integrator), is a fully functional universal remote that would take the place of ALL three remotes you currently have. The remote I would recommend is the Logitech Harmony- which is as easy of a setup as you can ask for.
The remote comes with an instruction booklet, and a cable that plugs into your computer. You go to the website the manual tells you to and then simply follow the instructions on the screen (it will actually ask you to select what TV, cable box and sound system you have- from drop down boxes), and then once you tell it what you have, you will simply hit "SYNC" and the remote will automatically program itself to your system and you can put all of the other three remotes away.
This remote is available at Radio Shack and Best Buy, or also can be purchased at the link below:
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