The best way to explain graphic differences between the 2 remotes is to have you download the ProntoProEdit NG software and import Daniel's 3000 PCF. You will then see the differences in how transparency is supported between the 2 remotes.
Yes, both remotes can control one system. However, you will most likely want to pick one remote (probably the 7000) and redo your config for it. Use the 3000 in the bedroom etc...