David,
[quote user="David Sabol"] I tried entering the name under "Linker command file" under the properties->general. But when I click OK and go back in to the properties, it shows as blank.[/quote]
I think this might be a bug in CCS 5.4. I observed similar behavior (the Properties->General showing that field as blank) and found that the linker command file was excluded from build even though it was actually added to the project. Do you see the linker cmd file grayed out as well in the Project Explorer denoting it is excluded from build? If so, try explicitly adding it back to the build.
The simplest way to add the linker cmd file to a project would be to just copy it into the project folder. Specifying it in Properties->General->Linker command file should work as well, and does in CCSv6. I think you just hit a bug in CCS 5.4.