No, that's how I created the connection in the first place. But I deleted it and started over for good measure. (Incidentally, it's confusing to have the quickstart panel launch a welcome screen that's not part of the project - it means the debug launch button and most of the other options get immediately grayed out because the welcome screen is not part of the project.)
Here's what the blue debug button finds:

Now, I believe those two entries represent the two different launchers. My question stands - what's the difference between the two?
I got the system stuck in a state where it wouldn't connect to the Cyclone the other day. It kept giving me an error about not being able to auto-detect and to specify the settings on the command line. I had to switch to a USB connection before it'd work again, and I think that's when I tried switching launchers.
Scott