The non-protocol communication can be set by the following two methods: (1) setting parameters using a programming tool, such as GX Works2, or (2) writing data to the special data register using a sequence program. (The program created is transferred to a programmable controller.)
A programmable controller operates in the same way regardless of a selected method. If both the methods are executed, the parameter settings are prioritized.
For details, refer to the following.

Section 5 of F. Non-Protocol Communication (RS/RS2 Instruction) in the FX Series Programmable Controllers User's Manual [Data Communication Edition] (Manual number: JY997D16901)