Yes just ticking the effect should start it enabled from then on.
If it's a preset the command in the ini file would be:
[GLOBAL]
Techniques=SMAA,
And that will make SMAA start enabled or what other effect or effects you want on.
The ini file itself with shader settings and these global settings is defined in reshade.ini or if that is not available it's [exename].ini
This line:
PresetFiles=C:\Program Files (x86)\ReShade\ReShade_Settings.ini