First of all, an upgrade is the best thing you can do, since FCKeditor is a retired product that is no longer supported. Its source code was frozen in 2010, no further updates are provided and as such, some issues may occur in modern browsers.
CKEditor is a direct successor of FCKeditor, and a very mature and far superior product. It was written from scratch based on our long experience and expertise gained while working on FCKeditor and it contains lots of new features and bug fixes as compared to FCKeditor.
However, since CKEditor was a complete rewrite of FCKeditor, with lots of changes in how the internal stuff works, no automatic upgrade path is available. CKEditor installation and configuration process is pretty straightforward, so if you were able to manage your FCKeditor installation, you should have no trouble with CKEditor either.
The best option is to download the latest CKEditor version and install it, starting anew. Play with the samples (available in the _samples folder), read the Developer's Guide for installation and configuration instructions and try to integrate the editor with your application.
If you would like to try to mimic your FCKeditor configuration in CKEditor, here is a matrix of the mappings between these two.