In a Basic MSI project, go to the Installation Information group, General Information view, Product Properties page, INSTALLDIR property.  When you create your Basic MSI project, InstallShield sets the INSTALLDIR path to include the Company Name and the Product Name.  Here is an example of the default path from one of my Basic MSI projects:

[ProgramFilesFolder]Wavepoint Studios\Mega View

Here, you see that the Company Name is Wavepoint Studios, and Mega View is the Product Name.  So, if you don't want the Company Name in your path, just remove it.

If you don't want the Company Name in the default installation folder structure, then go to the System Configuration group, Shortcuts view and look in the middle pane.  Under the Programs Menu folder tree, you will see a folder that is named after your Company Name.  If you don't want it in there, just take it out.  Of course if you do that, you will lose your application folder along with any shortcuts you have defined.  So, just drag the application folder to the folder directly above the Company Name folder and then delete the Company Folder.

In an InstallScript project, go to the Installation Information group, General Information view, Product Properties page, TARGETDIR property.  When you create an InstallScript project, InstallShield sets the TARGETDIR path to include the Company Name and the Product Name.  Here is an example of the default path in one of my InstallScript projects.

<FOLDER_APPLICATIONS>\<IFX_COMPANY_NAME>\<IFX_PRODUCT_NAME>

Here, IFX_COMPANY_NAME refers to the Company Name that the user entered in the SdRegisterUser dialog.  IFX_PRODUCT_NAME refers to the Name property in the Product Properties page.  If you don't want the Company Name in the TARGETDIR path, just take it out.

If you don't want the Company Name in the default installation folder structure, then go to the System Configuration group, Shortcuts view and look in the middle pane.  Under the Programs Menu folder tree, you will see a folder that is named after your Company Name.  If you don't want it in there, just take it out.  Of course if you do that, you will lose your application folder along with any shortcuts you have defined.  So, just drag the application folder to the folder directly above the Company Name folder and then delete the Company Name folder.

That's all there is to it.