Hi Barber,
MQX is setup so that the RTOS gets built up with libraries that are placed in the mqx/libpath.
The application you build will link against those libraries.
When debugging an application the header files and linker files that get opened are in the mqx/lib path. When the RTOS is built, the library and header files are copied from their source path to the mqx/lib path. So any edits you make to a header file in the mqx/lib path will get over written the next time the RTOS is re-built (this has happened to me many times...).
So when editing a linker or header file, always check the path (mouse over the file name in the editor window).
Your method of placing the linker script into your project is OK too.
From your reply I do not understand the error you are getting. Can you elaborate?
Regards,
David