lammert - 11:10 am on Mar 14, 2010 (gmt 0)
Copyright is something you have automatically, you don't have to register your software for it, although it may be useful if a conflict arises in the future. Patents on software are not recognized outside the US, and it would be doubtful that your system has such unique features that the benefits of a patent application for these features would outweigh the costs and time line involved. But if you think there are patentable features, be prepared to put some serious money aside and expect the process to take some to several years.
You didn't mention which programming or scripting language is involved. Some languages have the ability of precompiling with certain tools, and then encrypt, lock or license these precompiled parts.
As it is a CMS plugin, would it be possible to run the core code on your own servers with only an interface directly plugging in to the main system? This may involve some overhead and time delays, but you will still have the source codes on your system.