On metal roofs we always start with a rubber underlayment, then we trim the roof out, then we install the metal panels. $8 per sq. ft. for standing seam & $5 per sq. ft. for screw down on most jobs.
Metal roofs are a great way to go. They are stylish and out last most shingle roofs. They are lighter weight than shingle roofs too. For a whole house roof the standing seam looks better and is a life time product. The screw down is also a good product but is more for porches, garages, etc. and the rubber washers on the screws down does wear out over time. Either of these products are a good option for a flat roof.