In many situations, it is important to be able to switch to the source view in FCKeditor and add a few custom tags, needed for custom processing, or whatever. The problem is that browsers don't know how to handle non standard HTML tags, and usually break the DOM tree when finding them (specially IE).
To be able to load such tags in FCKeditor, maintaining their positions in the DOM tree, just use the "ProtectedTags" setting, listing the names of the tags you want to protect separated by a pipe (|).
Example: The following instructs FCKeditor to accept the tags <MYTAG> and <CUSTOM>.
FCKConfig.ProtectedTags = 'MYTAG|CUSTOM' ;