What machine will you be using to host the service? You need to install Add GTFS to a Network Dataset on that machine and then follow the additional instructions to "register" TransitEvaluator.dll with ArcGIS Server. ArcGIS Server is usually installed in C:\Program Files.
If the server machine doesn't have ArcMap installed, you won't be able to use the installer to install Add GTFS to a Network Dataset. In that case, I think you can just copy the folder holding TransitEvaluator.dll to the server machine: C:\Program Files (x86)\ArcGIS\Desktop10.[version]\ArcToolbox\Toolboxes\EvaluatorFiles.