It shouldn't be a problem to separate the Web server and the App server. You would just need to modify the file config.xml, located in C:\ProgramData\QlikTech\QvWebServer or C:\Document and Settings\All Users\QlikTech\QvWebServer. This file will contain all the settings for communications, including ports and tunneling. See pages 40 - 45 of the QVS Reference Manual for more details about this file.
