kjesmer It is certainly possible to get rid of CCMagic and install its contents the old-fashioned way, if that's what you want to do. Sims3Packs are placed in ...The Sims 3 > Downloads and installed through the launcher. Files with a .package extension go into ...The Sims 3 > Mods > Packages, no installation process required. But is this what you want? The point of CCMagic is to make things easier to manage, and launcher-installed content in particular can be difficult and annoying.
If you don't want to use CCMagic at all anymore, what I would suggest is converting all your Sims3Pack files (excluding Store content) to .package files. Delphy's Multi-Extractor does this, although there's a way you can without an outside tool as well, if necessary; it's just messier.
There are two reasons for this. One is that the launcher doesn't handle large amounts of content well, so limiting what it has to display to Store items helps a lot. The other is that .package files can be easily removed, either for testing or permanently, without touching any other content, whereas files installed through the launcher become bundles that are harder to work with and sometimes need to be deleted if one becomes corrupt or contains bad custom content.
You could delete the duplicates in CCMagic before proceeding, which is probably the easiest way to find them, but with everything in .package form, it may be simple to find the duplicates as well, depending on whether they're exactly the same files or two different forms of the same content.
So decide what you want to do, and I can help with that. But keep in mind that a big part of the reason to use CCMagic in the first place is the ability to disable what you don't want to use at the moment, which is not possible with the other approaches.