Certainly it's the smart thing to do (6)
I believe the answer is:
indeed
'certainly' is the definition.
(both can be used to answer in the affirmative)
'the smart thing to do' is the wordplay.
'the smart' becomes 'in' (as in fashionable).
'thing to do' becomes 'deed' (a deed is an action).
'in'+'deed'='INDEED'
'it's' is the link.
(Other definitions for indeed that I've seen before include "Absolutely" , "Truly or admittedly" , "In truth, in fact" , "still" , "To be sure" .)