The inner and outer probably refers to two bearings -"inner" being the one closest to the engine, and "outer" being the one closer to the propeller.
For the application you are speaking about I suggest you log on to some of the usual suspects for that size of boat and materials. A good place to educate yourself will be on the Morse Bearing website http://morserubber.com/
that will at least provide you with the proper descriptions of what they are referring to even if they use their own boatyard slang, or another good site for you to read about is Thordon Bearing at email@example.com
I don't think you are paying twice, but they may be talking composite bearing (outer bushing and inner bushing bonded together), or others where there is a brass bush fitted to your boat and a composite material is pressed into that which "holds" it. The composite material is water lubricated and your shaft actually runs in that.
Usually the argument is around the wear-down or clearance between the shaft and the bearing material with boatyards. They say it needs replacing because they say it is too much etc....their are certain rules of thumb that are used and generally they favor the shipyard. You need to provide the size of shaft, the RPM, the measured wear-down in the bearings (hence the clearance).
Either way you will be smarter than the average boater when you are done with all this.
I hope this helps.