Sorry to hear about the recent issues you have been experiencing.
There is going to be a learning curve involved with this setup. I will do my best to explain.
Please read these articles for setting up External MIDI Devices with Studio One 3:
http://support.presonus.com/hc/en-us/articles/115001352966-Studio-One-3-How-do-I-setup-a-hardware-keyboard-synthesizer-in-Studio-One-3-
All of your keyboards with built in sounds you want to use with Studio One HAVE to be set to external MIDI clock. Studio One has to be the master MIDI clock in all scenarios. Go into the options for each of these devices and set them to use Extenal MIDI clock.
1. For the piano keys of the Keylab 88 and the Nord Lead 3, create for each a New Keyboard, with the MIDI "Receive From" assigned to the relative MIDI port the device is connected to. You don't need the MIDI "Send To" set. Don't check any of the MIDI filters, only check filters if you want block a certain MIDI message. The "New Keyboards" you set up here can be used to control internal VST's or to control the External MIDI devices you will set up in step 2.
2. To use the built-in Sounds of the Nord Lead 2, JD990, Supernova 2, Kawai K4r and a Proteus, you will need to create for each of these a New Instrument with the MIDI "Send To" set to the related MIDI port. Check ALL the MIDI clock options for each device. By default, New Instruments have ALL MIDI channels selected. If you are doing any sharing of MIDI ports or "MIDI Through" configs that use the same port, be sure the choose the MIDI channel in this screen, not all MIDI ports. Also, make sure the external device has the same MIDI channel selected.
3. Once you have a instrument track setup in a New Song, for the MIDI IN you choose the device you want to use, this will be one of the keyboards you set up in Step 1. And on that same track, you choose the MIDI OUT device. Which will use the Instrument you setup in Step 2. The following article goes into more detail on setting up to record using an External Device: Setting up to record with an External MIDI Device Studio One:
http://support.presonus.com/hc/en-us/articles/115001418283-Setting-up-a-Song-to-Record-With-External-MIDI-Devices
4. All of the devices that have built in sounds will need to be routed audio wise to your audio interface that is set in Studio One. You can blend this all together like you mentioned using your mixer, but when it comes time to bounce MIDI to audio, there may be some issues. I definitely advise getting and an audio interface that has at least 8 audio inputs. You can use the Saffire 6, however, it only has what looks to be 2 inputs. This will be tricky on bouncing.
5. In regards to the question about sound that is recorded onto a track...... If you have all your external MIDI devices audio outs routed into your mixer, and the mixer connected via a stereo connection to your Saffire 6, When you playback MIDI, all the audio will be coming back in to Studio One ONLY through the 2 channels that the Saffire has. You will have to do some muting to bounce instrument MIDI to audio. This is why I suggest at least and 8 channel audio interface.
As this can get very complicated, if you still have questions please create a ticket to technical support. 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.
Best regards.