Noone wanted to help the newb - eh? j/k. I figured it out. I went ahead and installed btsync on that users directory. Even though I used the configuration file to start the second process, the webgui did NOT work (yes, I changed the port). Therefore, I had to hardcode the folder settings and secrets in the text file. It works for now, and I understand that this is an alpha release. Just wanted to share my experience on linux (Ubuntu Server 12.04 LTS).