You can use the clicked signal because it is only emitted when the user actually clicked the check box, not when you manually check it using setChecked.
If you just don’t want the signal to be emitted at one specific time, you can use QObject::blockSignals like this:
bool oldState = checkBox->blockSignals(true);
checkBox->setChecked(true);
checkBox->blockSignals(oldState);
The downside of this approach is that all signals will be blocked. But I guess that doesn’t really matter in case of a QCheckBox.