It depends if you are planning to hike up to the top, or you one of the lazy b**stardos (like me), that usually use cable car.
In first case, I'd suggest to go there early in the morning. Depending on how fit you are it should take four to six hours to get to the top. (alhought in early years those who were transporting building materials up to Säntis could do more than one trip to the top

)
If you don't plan to hike up there, I suggest to combine Säntis with other activities, like visiting Appenzeller and having dinner there.
It takes 1.5 hrs to drive to Säntis. Cable cars to the top are very frequent and take only few minutes. (Check the weather before going there, it's a waste of money to get up there if the top is hiding in a cloud.) I didn't particulary like the restaurant up there, and if you won't visit it in about 1-1.5 hours you'll be heading down.