Hello Stu,
I am not sure I understand your question, but I will do my best.
When you FTP to your RT controller via just ftp://192.10.10.53/ this corresponds to "C:\" on the RT controller's hard drive (compact flash). So when you are in ftp://192.10.10.53/NI-RT/SYSTEM/ this is the same as "C:\NI-RT\SYSTEM\" on the remote hard drive. Conversely, referencing "C:\test\test.iak" in your code would correspond to a file "test.iak" in the ftp://192.10.10.53/TEST/ folder. Just remember that any code that refers to a file and is running on an RT target is going to be looking for that file on the RT target's hard drive, not the Windows computer's.