A second bird at the back of ship (6)
I believe the answer is:
astern
'at the back of ship' is the definition.
(I've seen this before)
'a second bird' is the wordplay.
'second' becomes 's' (common abbreviation).
'bird' becomes 'tern' (tern is a kind of bird).
'a'+'s'+'tern'='ASTERN'
(Other definitions for astern that I've seen before include "Toward the tail of a vessel" , "Towards rear of a vessel" , "The wake is" , "Ran set (anag.)" , "Aft" .)