Remember that the gui (Fantasia or Qsampler) will only allow you to edit the first plugin instance. Any more and Fantasia will show the midi and audio plugin instance "devices", but won't allow you to add or modify channels for instance number 2 onwards.
I dearly wish I had the skills to write a proper LV2 and VST plugin interface for linuxsampler, as it's my main instrument, driving all my orchestral sample libs, but I don't. Even something like the DSSI GUI, LS16, but with the ability to save presets. (LS16 won't save them, something to do with DSSI according to Tim from Muse)
For Reaper, and if you wish to add many VST instances, you'll need to do it one track template at a time. (And Reaper does remember the data for the loaded instance).
Add a new track.
Add an instance of Linuxsampler VST
Open Fantasia in a terminal
Add all your instrument channels and instruments
Close Fantasia
Go back to the track and after making sure all your routing/Monitor/Record/RecordArm/Trackname is done, save it as a track template.
Go to the plugin instance in the FX window, save the preset as..
Save as Track Template again. (Save,save,save)
Remove the track.
Wash, Rinse, Repeat for as many instrument/plugin instances as you need.
I have 89 so far, with a few bits and pieces still to do, that aren't important at the moment.
The effort is worth it, imho, although it's definitely grunt work for the lack of a gui.
Onwards and Upwards.
Alex.