If you intend to use the whole map, there is no requirement to create a sub-map. Just go through the motions of creating a new scenario, and when it asks for which map you intend to use specifiy the main *.map file. The scenario will be created with a "naked" map. Mines, impassible, etc are all scenario-specific (not map-specific), so if you create a fresh scenario you start with nothing.
As for editting fatigue, etc, stack by stack is it, although you can also edit the *.scn file directly (although to edit more than a couple of units that way would probably be difficult than using the game scen editting GUI), or you could use the "PzC NEW Scenario editor" available at
Glenn's site. Be a bit careful with it though - it seems to me that with very large scenarios (in essence: full campaigns) it gets confused and arbitrarily deletes chunks of the file.
Regards
JonS