It all depends on how often you are going to use that Kontakt drum kit.
In your position I would put some work in to create a multi-output drum kit within Kontakt. That will make life much easier, and you can capture all the kit pieces separately, all at once, in Reaper.
-- In Kontakt's Mixer, create all the channels you need (you can always add more later), name them "Kick", "Snare", "Toms" etc as desired and route them to sequential pairs of outputs (1|2, 3|4, 5\6 etc.)
-- In Kontakt's Mixer, save the config as an Output preset
-- now load your drum kit, by default all its output goes to the first Mixer channel and so to plug-in output channels 1|2.
-- open the Instrument Editor by clicking the "wrench" ("spanner") button,
-- open the Group Editor by clicking its button
-- there (in a cramped window) you will see the various groups for the drum kit samples,"Clap", "Bass drum", "Snare left" etc.,
-- click on a name of one of the kit pieces to select it, then click the check-boxes of other kit pieces that you want to send to the same output,
-- in the Amp section, select the desired output, then deselect the groups
-- repeat those two steps for the pieces you want to send to each output.
When done, close the Instrument Editor and Save the drum kit with a slightly different name.
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Now, back in Reaper, open the FX panel on the Kontakt track,
-- make sure Kontakt is selected,
-- click [Options] then "Build multichannel output ...."
-- this will create output "audio" tracks for you and route the Kontakt plug-in outputs to them,
-- select those newly-created tracks, RecArm them and set them to Record Output (Stereo),
= put your MIDI item (with all of its notes!) on the Kontakt track and hit Record.
Here in Kontakt 4 (!) I am assigning three groups to the SNARE output:
And here I have recorded the different drum kit pieces to separate tracks:
^^^^
In case you're wondering, I did not change the output for the Hats, so they are recorded on the Kick track.