Note king having trouble with emperor (6)
I believe the answer is:
mikado
'emperor' is the definition.
(mikado is a kind of emperor)
'note king having trouble' is the wordplay.
'note' becomes 'mi' (as in do-re-mi).
'king' becomes 'K' (chess abbreviation).
'having' is a charade indicator (letters next to each other).
'trouble' becomes 'ado' (both can mean bother or commotion).
'mi'+'k'+'ado'='MIKADO'
'with' acts as a link.
(Other definitions for mikado that I've seen before include "G&S emperor" , "national leader" , "one of 63 [OPERETTAS]" , "Gilbert and Sullivan's emperor" , "mperor" .)