"You can load just MidiLooper into a midi track but you will only have the available midi devices to choose from. "
If you set Kontakt as default synth,
go to Midi Button > Midi Drivers check Use VSTi/DXi Synth
Choose Kontakt, close window
Go to Plugins Button > VST/DXi Synth Settings to Edit the VSTi
Load a Kontakt Instrument set Midi in Ch to the same channel as MidiLooper track channel, load the next Kontakt instrument for the next track/channel in MidiLooper.
Before dragging any newly generated midi into a new MidiLooper track you can change the channel first in BB Prefs - Channels then set MidiLooper track channel the same and the Kontakt instrument.