I logged on to IRC and received some help in setting this up here's what I've learned so far.
1. Right click on the crosshair icon for innerspace and select configuration. (Box Computer)
2. Enable incoming connections and click apply.
3. Restart IS and check to make sure your change applied properly.
4. Before closing the screen notice the Unique name for this uplink.
5. Locate the eq2botcommander.iss file in the scripts directory on the controlling computer.
6. Edit the file and enter the Unique name you found above for the first computer.
7. Save.
8. Load up EQ2 and load up eq2botcommander.
9. Enjoy.