All Programs->Wacom Tablet->Wacom Tablet Properties. you change settings per app in Wacom Tablet Properties. just make sure the apps is open when when you make a new profile. no need for scripting etc.
What tablet are you using? I use a Wacom Bamboo Pen myself and you only get the cheap drivers that are not able to do profile management. I made a small profile manager with batch and autoit scripts (alternativly vbs works too) to change between them. You can even switch monitors with it. I use the "G"-Key's of my G15 to…