Manage firm used by Royal Navy in Cheshire town (7)
I believe the answer is:
runcorn
'in cheshire town' is the definition.
(I've seen this before)
'manage firm used by royal navy' is the wordplay.
'manage' becomes 'run' (I've seen this before).
'firm' becomes 'co' (a firm is a company).
'used by' means one lot of letters go next to another.
'royal navy' becomes 'rn'.
'run'+'co'+'rn'='RUNCORN'
(Other definitions for runcorn that I've seen before include "Mersey town" , "Cheshire industrial port" , "Industrial town in Cheshire" .)