Let's get some more details for your equipment:
Your signal: I'm assuming that you are plugging your guitar into a pre-amp and some sort of analog to digital converter (or an interface that does both).
That signal is being captured by a Track within Studio One.
On that track you have inserted Amplitube and adjusted the sound to taste.
Now you want to be able to control the knobs within Amplitube with your Shortboard by plugging it into a USB jack on your computer.
It is basically a MIDI controller (much like keyboard controllers), and as such you will want to add it to Studio One (Ctrl Comma)
Question: Do you see it and/or are you able to add it to your devices within Studio One?
indicates that you can assign each of the controls to a MIDI note.
So then you need to "wire up" those MIDI notes with the knobs within Amplitube.
If Amplitube supports automation, you can use the "MIDI learn" capabilities within Studio One to do that "wiring".
(It'd be easier if there was already a "Line 6" entry within the "Add a Device" list)