Begin with the E in “ale” (3,3)
I believe the answer is:
set out
'begin' is the definition.
('set out' can be a synonym of 'begin')
'the e in ale' is the wordplay.
'in' indicates putting letters inside.
'ale' becomes 'stout' (stout is a kind of ale).
'e' going into 'stout' is 'SET-OUT'.
'with' acts as a link.
(Other definitions for set out that I've seen before include "Depart" , "Commence journey, or make beginning" , "Begin a journey or arrange display" , "State" , "arranged" .)