Sory for asking but I'm still confused about directories :) After copying I should have the tree like this:

~fckeditor/editor/plugins/equation/equation/*all files form "equation" directory*
~fckeditor/editor/plugins/equation/tagprocessors/*all files form "tagprocessors" directory*

or like this:

~fckeditor/editor/plugins/equation/*all files form "equation" directory*
~fckeditor/editor/plugins/tagprocessors/*all files form "tagprocessors" directory*

Also in the first line

FCKConfig.Plugins.Add( 'equation', 'en' )
FCKConfig.Plugins.Add( 'tagprocessors' ) ;

";" is missed