You need to define the following variable in your standards.cfg file..for example I used to have mine set as below. Though i find it is easier just to create a standard project directory and copy this and it's pcf file for every new project as you cannot stipulate that the new project command creates lib files also...
_USTN_PROJECTSUBDIRS = building
_USTN_PROJECTSUBDIRS > drg's
_USTN_PROJECTSUBDIRS > ext info
_USTN_PROJECTSUBDIRS > feasabililty
_USTN_PROJECTSUBDIRS > images
_USTN_PROJECTSUBDIRS > pdf's
_USTN_PROJECTSUBDIRS > planning
_USTN_PROJECTSUBDIRS > survey
likewise if you want sub folders you just add them as such:
_USTN_PROJECTSUBDIRS > planning/dgn
hope this helps
I never heard of using a different file that can be used, but you can open "project.template" in any texteditor and edit it the way you want it.
Alternatively you may copy existing *.pcf and just rename them.That is what I do. Most of the time my most recent *.pcf is my best configuration. Instead of copying it´s content in "project.template" I just copy it to the new projects name.
For the same reason I prefer copying a default project structure to the new project directory as DGammie mentioned.