I believe you are referring to the relationship between the generator settings page and the advanced commands one can specify in a custom frequency set.
If this is correct, then the settings stipulated in a custom frequency set will take precedence.
For instance if I specify no gate in the generator settings page for a preset, but the preset consists of a frequency set with the G1 command, then gating will be enabled for that frequency set. The rate of the gate will still take its value from what is specified in the generator settings page.
If my default amplitude for the program is set to 20v in the generator settings page, but my frequency set has the command A10, for this frequency set it will use 10v.
Most of the commands are either frequency set or program altering. For instance if I specify a square wave in the generator settings page, but in my first frequency set I specify W1 to use a sine wave, then the rest of the entire program will use a sine wave (last I tested this, I'm not sure if the code has been improved since to switch waveforms mid program).
The commands F and C are frequency specific and can be used multiple times through out a frequency set and or program.
Best practice is to setup your generator settings to a safe default and be aware of any overrides that are in a frequency set and how this may affect the program.
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