Hello,
There is a module configuration table for those merge modules. I do not know how this works in Installshield. I can tell you how it works in Visual Studio and Wise.
In Visual Studio they set the TARGETDIR property be the application install location, therefore the default installs to the same directory as the application. You can change this by highlighting the MSM and setting the RetargetableDirectory property in the property pane to wherever you think is best.
In Wise, when you add the merge module it asks you for the configuration of the RetargetableDirectory, so you specify where you want that directory changed to. This is stored before the build in a WiseModuleConfiguration table.
At the least you can change the property using a custom action:
DIRCA_NEWRETARGETABLEPROPERTY1.FFD3184641DF4FD592EF03A8BF6B1E0F 307 NEWRETARGETABLEPROPERTY1.FFD3184641DF4FD592EF03A8BF6B1E0F [MyApplication]
This is a custom action that will change the property for Common to install to the "MyApplication" folder.
I hope this helps you.
Jeff
NI