Simply add Weaponiser to a midi track. Create four new audio tracks, and rename then to receive the audio from each engine (e.g. Onset, Body, Thump, Tail).
Click and hold on the ‘Route’ button in the track containing the Weaponiser plugin. Drag the icon which appears to the ‘Route’ button on each track you would like to route to.
Click on the ‘Route’ button in the main Weaponiser track again. A menu will appear. In the ‘Track Channels’, select ’10’ from the drop-down menu. In the section for sending to the Onset track, click on the ‘Audio input’ section (it should read ‘1/2 ‘ by default). Under ‘Stereo source’, select ‘3/4’ (this will route the outputs from channels 3/4 from Weaponiser to this track). For the ‘Body’, do the same, only select ‘5 /6’. For ‘Thump’ select 7/8 and for ‘Tail’ select 9/10.
For each track, click on the Input selection icon, and choose ‘Record: output > Record: output (stereo)’
Arm these tracks.
Press ‘Record’ in Reaper’s main transport, and fire Weaponiser’s main ‘Fire’ button from the UI, or trigger a midi note at C5. This will trigger all the engines in the plugin (if none are muted or soloed) and route the audio to the individual audio tracks you have setup, and record the output to the timeline.
To render or export these tracks, solo one at a time, and export as normal.