You need to read the manuals to see if it's possible. I think the remote had a small switch behind the battery that allowed me to switch between the three code sets, and it might have been necessary to press a combination of keys on the unit itself to get it to understand what codes to expect - but it was all in the manual. Have a look and see whether it's an option on either amp or CDP.
(If neither gives this option, you could always block off the amp's IR sensor and just use its front panel controls and just use the remote for the CDP. Not ideal, but there aren't a lot of options if you want to keep both. A quick google suggests that there's an option to disable the IR sensor in the CDP, and that the amp has a menu setting to use its rear IR inputs, which would effectively disable the front sensor. It doesn't look like either has the option to change its code set, so it may be that if you want to keep both, you can only use remote control for one, disabling it for the other - don't take that as gospel though, do read the manuals!)