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  1. How can I configure my virtual directory to have Windows Integrated Security checked and Anonymous checked through installer.

  2. How can I assign my newly created Virtual directory to an specied appPool which is already created on IIS6.0?

Any code snippets and how to perform these action thru maybe a Custom Actions Editor/ any web sites would be greatly appreciated.

A: 

I can't give you a full answer to this, other than to take a look at Windows Installer XML (WiX), which I've recently started looking at. The two links below give a starting point for some snippets of code for WiX

The Setup/Installer projects in VS2k8 aren't particularly extensible (at least that I've found!) so changing to something like WiX is probably your best bet. A bit of a step learning curve, but hopefully what you're after.

Rob

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