lost in arcgis

yes arcgis is a huge package. For the beginner its just overwhelming. Fortunately the tutorial from PASDA helps.

Try to publish a GIS resource on the other hand. Sucks. When you edit a map from ArcMap then save it, the location of the shape data (.shp) is stored in the .mxd file. Thus you have to make sure that same location exists and has the file otherwise a "The database was not found" error will appear in the logs and no layers.

The only way is to recreate the same directory structure as the server ie the default c:\arcgisserver directory and subdirs.