I use left and middle as port and starboard throttle (if two engines), or just the left one when on a single engine vessel. Right lever just stays fully down or at 50%/idle/stop to make it easier to find the right position for the throttle levers. If youre just going to use the TQ for ShipSim I'd consider just removing one of them (perhaps the middle?). They are probably not intentionally removeable, but I'm sure a screwdriver and/or excessive use of force will solve that issue. For the more technically inclined, it is probably not THAT hard to remove the entire assembly of one of the levers with potmeter and all, extend the wires and put it at a 90 degree angle - voila, bowthruster control.
Ok, a small edit: First of all, there is a thread on the Ship Control Unit over at the SS08 boards, link (http://80.95.161.114/shipsim/forum/index.php/topic,16476.0.html).
Secondly, I noticed that someone mentioned that SS08 only supports one joystick. I must have used some sort of tweak or thirdparty software to get it to accept both my G-25 and TQ. I cannot remember any of that as I've had it running since a very long time. I recently moved (again) and where I live now I do not have the space for a hardware setup like that just yet (the ship control unit on the other hand might just fit!) so I cant offer to figure out what exactly I did either. Just wanted to give anyone wanting to run two joysticks a little heads up.