I referred to the default installation paths. If you are not on the default, substitute as necessary.

What I meant was select the ISBoxer node at the top of your profile, and then set the Innerspace folder.
It
might complain that your GameConfiguration.xml file is missing (it did when I tried it as above). This is because it will be in the Innerspace folder. You
might need to copy it to the x64 folder. Probably not though if you have normally configured Innerspace to run the x64 version. You will need to try it.
The reason I suggested the above is because when you then launch from ISBoxer, or create desktop shortcuts, it sets it up to use the above folder as the launch location, and use the Innerspace.exe in the x64 folder.
You shouldn't need to move dll's or anything else as the appropriate x64 versions will already be in the correct location. It is only the potential for
some of the xml config files that might need to be copied. I would just do them one at a time as they get whinged about.
edit:
A test shows the following get whinged about.
ISBoxerToolkit.GeneralSettings.xml
ISBoxerToolkit.RepeaterSettings.xml
ISBoxerToolkit.MenuManSettings.xml
ISBoxerToolkit.KeyMapperSettings.xml
ISBoxerToolkit.Clickbars.xml
These are actually in the Innerspace\Scripts folder. I copied the Innerspace\Scripts folder to Innerspace\x64\Scripts and it all worked for the export, and the launch appears to be good. This is the only thing I needed to copy.
A Symlink might be a better option than copying, but idk.