The manual transmission will provide better fuel economy around town, but the automatic will likely get better fuel economy on the highway, due to its taller gearing, unless you regularly do engine off coasting in the manual.
With many ecomods and slow, careful driving, my '04 auto Civic had a best highway trip of a hair over 60 MPG for over 300 miles. To get that kind of mileage in the city required extreme hypermiling techniques.
To beat the auto's highway fuel economy you would need to use a taller geared transmission.
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2013 Toyota Prius C 2 (my car)
2015 Mazda 3 iTouring Hatchback w/ Tech Package (wife's car)
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