In the Parse Server documentation, some notes related to GeoPoint are described.
At the moment, each Parse.Object class can have only one key with a Parse.GeoPoint object. In order to have more than one GeoPoint per class, we recommend using Pointers.
Basically, you can create another class, it will be pointing to your target class, and then, you can have a column with the Pointer type in your target class. This new class will store the other column of the GeoPoint type.
You can learn more about Pointer with our Parse Crash Course on it.
If you have any other questions, please contact us.