In order for the water in the aquarium to be safe for your fish, it needs to keep up an appropriate flow. The filter in your aquarium should be passing through all the water in the tank at least three times per hour, which is quite a lot. So basically, your aquarium filter should ideally be running constantly, non-stop.
Especially because there are no real issues with over filtering (apart from the expense and cost that it causes). While under filtering, on the other hand, leads to many health issues for your fish, and can seriously damage the bacteria levels within the tank.
If you want to keep your fish as healthy as possible, it is recommended that you try and keep the aquarium filter running 24/7, non-stop.
Leaving the aquarium filter off overnight is a big no. The filter should never be off for more than 5 hours or so. And as to answering how often to run the aquarium filter, the answer is just basically as often as possible.