US city is organised, not run badly (3,5)
I believe the answer is:
san diego
'us city' is the definition.
(I've seen this before)
'organised not run badly' is the wordplay.
'not' indicates named letters should be taken away.
'run' becomes 'r' (cricket abbreviation).
'badly' is an anagram indicator.
'organised' with 'r' removed is 'oganised'.
'oganised' is an anagram of 'SAN DIEGO'.
'is' acts as a link.
(Other definitions for san diego that I've seen before include "Pacific port" , "California naval port" , "US city" , "Californian port" , "Calif. naval base" .)