Sorry just got home. Ok here are the steps you fallow to set this up. You can then use the plugin on an FX track or as an insert on an audio track.
1. Pull up audio connections (Studio--->Audio Connections....)
2. Navigate to the External FX tab.
3. Hit the "Add Exteranl FX" button.
4. Name the FX, in your case I would call it "Strymon Flint"
5. In the case of this pedal I would personally set it up as Mono Send Configuration and Stereo Return Configuration.
6. Hit the "ok" button.
7. Now you have to connect your I/O the effect is using. Your Send bus should be the output you have on your audio interface that goes to the pedal. This is hardware dependent, so only you know what is correct here.
8. For the return bus, if you set it up as a stereo bus you need to set those 2 as the inputs you have the pedal connected to, again this is hardware dependent so only you know what is correct here again.
Once you have done this, cubase will create a folder in your plugins list. It will be called "external FX." Inside you will have a "plugin" (not really a plugin, but it loads like one) that handles the gain of both the send and return as well as the ping feature. The ping feature is the little sawtooth icon button at the top right hand corner of this "plugin."
To ping the signal path, hit the button with the pedal TURNED OFF but still passing signal. The idea is to have cubase measure how long it takes the loop to complete and compensate for the latency, it can't do that if the ping is wet with reverb. Also as stated above, you will want to re-ping any time you change your hardware buffer settings or TBH I would do it every time I opened the project to work on it.
Let me know if you have any questions.