What is the box to the right of the simulation represent? This makes me feel like I have something setup wrong. I've never been able to get my soft limits configured and I'm wondering if this may be a reason why?
Thats the machine extents. Remember to Home to make reality line up with the view (if that doesn't happen you aren't running standard Grbl, or you have Homing Dir set incorrectly)
Then you should have standard firmware. You'd probably know if you flashed something non-standard to it using some 3rd party instructions or a custom compile
As mentioned above Remember to Home, or recheck your Homing Dir settings. Have a read through the Grbl Wiki at github.com/gnea/grbl/wiki