Once you have all the Windchill stuff copied you will probably want to go back and copy the shortcut to launch a Windchill shell. I also configured everything to run as a service. You can do this from a Windchill shell:
REM Install Webserver (Apache) as a service
cd E:\ptc\Windchill_10.2\HTTPServer\bin
httpd -k install -n "PTC Windchill Web Server"
REM Install Windchill Directory Server as a service
cd E:\ptc\Windchill_10.2\WindchillDS\server\bat
windows-service -e
REM Install Windchill Method Server as a service
cd E:\ptc\Windchill_10.2\Windchill
ant -buildfile opt\ntservice\WindchillService.xml install -DserviceName="PTC Windchill Method Server"
REM Add startup dependencies to method server service
sc config "PTC Windchill Method Server" depend= "PTCWindchillWebServer"/"PTC Windchill Directory Server"