Sorry to hear about the recent issues you have been experiencing.
Here is a guide from Akai on setting up their devices with Studio One: http://www.akaipro.com/kb/article/1590
Basically you will need to create a "New Keyboard" in Options/Preferences(OSX) > External Devices. This will be for the drum pads. Make sure in this New Keyboard to not place check marks by any of the filters. This will disable the ability for this device to send certain MIDI messages.
Then create a New Control Surface for the surface controls of the unit.
Here is another great article in that regard: http://support.presonus.com/hc/en-us/articles/210040463-MIDI-External-Devices-Control-Surfaces-Setup
If you have further need for discussion on this issue, please submit a support ticket.
We also encourage you to create a thread about this on the Presonus user forum. https://forums.presonus.com/viewforum.php?f=108 This will allow for back and forth discussions about an issue or question and more points of view as to possible different approaches or workflows.