At which one is confused, in the main? (3)
I believe the answer is:
sea
This clue is a double definition.
'at which one is confused' is the first definition.
('at sea' can mean confused)
'in the main?' is the second definition.
(the main is an old name for the sea)
(Other definitions for sea that I've seen before include "The drink" , "Lesser ocean" , "Cause of flooding" , "E.g Aral or Weddell" , "Body of saltwater" .)