They command outer garments to cover underwear (3,5)
I believe the answer is:
top brass
'they command' is the definition.
(military commanders or superiors)
'outer garments to cover underwear' is the wordplay.
'outer garments' becomes 'tops' (tops are garments worn over other clothes).
'to cover' indicates putting letters inside.
'underwear' becomes 'bras'.
'tops' placed around 'bras' is 'TOP-BRASS'.
(Other definitions for top brass that I've seen before include "Senior military personnel" , "high-ranking officials" , "management" , "Leadership" , "most important officials" .)