I don't think there are any specific hook points either in the InstallShield task (thus not the .isproj either), nor in the automation layer, for chained packages. However the data in the ISChainPackage and ISPathVariable tables are fairly straightforward if you are willing to edit it with Windows Installer automation (or MSXML if that's your storage format). Then again, if you set up your path variables correctly, perhaps you can use that hook point...
If the above don't work for you, I'd suggest a page from Chris Painter's book wherein you'd set up the ISM to reference a staging path and have the preceding part of your build process copy the desired package into it.
