Well, the functions of the two systems aren't exactly mixed together in Denise. There are two main-menus named "C64" and "Amiga," with the respective sub-menus for each system located underneath them. Incidentally, you can also disable one of the two systems (emulation cores) in Denise, if you don't want to have it visible. To do this, go to "Options/Settings" and then navigate to "Core Selection" and disable that system, you don't want to have, then it's menus won't appear anymore.
Therefore, you can also set it up in a way, that you have two seperate instances of Denise on your PC. One emulator instance running as a C64 emulator then and the other as an Amiga emulator. Additionally, you can detach one of these two instances from automatic-updates, for example, the Amiga instance via "Amiga/Configurations" and then "Undock". This then allows you, to configure both of these instances independently and differently, as undocking causes that instance's settings-files, to be copied directly into its own folder on your PC, while the setting.files of the other instance remain under "Admin/AppDate/Roaming/Denise". When you then eventually update that version sometime, you can simply copy those setting-files over to the new version's folder, manually.
Really alot of things are possible in Denise. You should also read the unofficial short-manuals, in the MISC section of the Denise Sourceforge website. There are good tips to some functions. But okay, this website here, is about the Adrian C64-game, therefore, back to it. :-)