It's fairly easy to use Reaktor as an effect. It's a little different than using Reaktor as an instrument. First you need to make sure that your MIDI track is routed to an instrument. In the image below I have a MIDI track and Presence XT is inserted as the instrument. If the MIDI is not routed to an instrument first, there will be no audio to process with a Reaktor effect.
Then you need to navigate to the Reaktor FX plugin in the Effects menu. NOTE: This is different than inserting Reaktor as an instrument. You can be sure you are using the Reaktor FX plugin when you see the FX in the name of the plugin.
After that, all you need to do is insert Reaktor FX as an effect insert for the Presence XT channel and then load the Reaktor effect ensemble inside of Reaktor. Here you can see that I inserted Reaktor FX in the Presence XT channel and have loaded the Echomania effect ensemble.
You could also use a bus or FX channel. The only difference is that you would then have to enable the send in the instrument channel.