to change the team color and stripe color, either batch run the script hw_color_change (put in scripts-trusted) in paint shop pro 
after setting the rgb values (read the comments in the script for the values to change) on all the .psd files, having it save each one as a .bmp

or
open each file in any program that can edit .psd files and change the layers col1 (team color) and col2 (stripe color) to the color you want
and save as a .bmp

once you have done that, open the .pdo in pepakura and go to 3DModelWindow>Set Texture and change each material to the correct .bmp


Material #		Image
1			frontlowerantenna
2			frontupperantenna
3			bridgeback
4			page1
5			page0
6			sidemidlower
7			veryfront
8			page2
9			botmid
10			front_face
11			sidemidlowsides
12			bridgefront01
13			siderear
14			bridgesides
15			engine
16			frontantennabase
17			botrear
18			toprear