"best two scores of the entire day" is never used.
The options we have are:
1. Best single run of the day
2. Best run of morning plus best run of afternoon
3. Score morning and afternoon as separate events
We usually use best run of morning plus best run of afternoon, since it allows for changing conditions and also allows for a course change at midday. The downside is when we have something like the upcoming event where there is a novice school on Saturday morning. If they move over to the main course in the afternoon, their scores will all show as DNS, which makes for much unhappiness.
Whatever we decide for the day, it should be announced at the driver's meeting in the morning. Unless we have a good reason to change it, a championship event will be scored as best run of morning plus best run of afternoon.