No, you don't have to do it manually.
The storms and black hole systems do masking by default.
quote:
Name := Standard 3
Description := Standard solar system.
System Physical Type := Normal
Background Bitmap := Starmap.bmp
Empires Can Start In := TRUE
Mask Background Objs := FALSE
this is from systemtypes.txt. That Last entry is the relevant one. Just go in and change that to TRUE for the system types in question, and you're good to go.
Phoenix-D