Piloted in over a city in Spain (6)
I believe the answer is:
toledo
'a city in spain' is the definition.
(city in Spain)
'piloted in over' is the wordplay.
'piloted' becomes 'led' (pilot can mean to lead or guide).
'in' means one lot of letters goes inside another.
'over' becomes 'too' (I've seen this before).
'led' inserted into 'too' is 'TOLEDO'.
(Other definitions for toledo that I've seen before include "Sword; city in Ohio" , "Looted the Spanish city badly" , "Blade" , "Spanish city, famous for steel and swords" , "To dole out in the Spanish city" .)