None of the current Wise products offer official support for Visual Studio 2008 or its derivatives, so you may run into problems, but these may be surmountable using existing Windows Installer functionality.
Things like the DLLs used in the patching engine in the Wise editors are going to be massively out of date, but you can update these MS dlls from the latest windows installer SDK, which you can download from Microsoft.
The only real advice I can give you is to test, test and test again. If you have a specific issue, search the Altiris KB and/or post here.
Google also offers a powerful search capability that can identify known issues in creating MSI deployments for .NET packages, and offer workarounds, whatever tool you are using.