Drink with naval officer: remain seated with one in theory (11)
I believe the answer is:
supposition
'theory' is the definition.
(I know that supposition is a type of theory)
'drink with naval officer' is the wordplay.
'drink' becomes 'sup' (to sup is to drink).
'with naval officer' becomes 'position' (I am not sure about this - if you are sure you should give a lot more credence to this answer).
'sup'+'position'='SUPPOSITION'
'remain seated with one in' acts as a link.
This may not be correct. Some or all of it may belong to another bit of the clue.
Can you help me to learn more?
(Other definitions for supposition that I've seen before include "suspicion" , "It's taken for granted" , "Surmise" , "Assumption, hypothesis" , "theory" .)