It's in different ways that they're cleverly amusing (4)
I believe the answer is:
wits
'they're cleverly amusing' is the definition.
The definition suggests an adverb but the answer is not.
'it's in different ways' is the wordplay.
'in' means one lot of letters goes inside another.
'different ways' becomes 'ws' (I am not sure about this - if you are sure you should give a lot more credence to this answer).
'it' going into 'ws' is 'WITS'.
'that' acts as a link.
Can you help me to learn more?
(Other definitions for wits that I've seen before include "Wags, quipsters" , "Senses" , "Humorous people" , "Canniness" , "Keep them about you to stay alert" .)