The TOSBS seems to have some cloned attributes from The BStar and Bay and shares the same front dock position, so it's at least a couple 100 meters away and to the right. It is basically a station keeping type of dock. I just looked and I'm right they have the same dock configuration but it is written in the Vessel Config so it's easy to change:
BEGIN__DOCKLIST
66.615 -12.338 816.69 0 0 1 010x,y and z x is up and down, y is back and forth, z is bow to stern. Using this formula you can see why it is to the right looking down the nose (-12.338, 0 would be in the middle and 12.338 would be in the same position but to the left. To get the ship closer to the target change z (816.69) to a smaller number, say-at a guess 616.69- this will bring you closer. Play with these numbers to get desired results, and this is true for attachments as well. You can also add a docking port or ports to other ships doing this, say you want a docking port in front of the bay door on the QJFF. Just add this line to the vessel config and play with it till it's right and there you go. So 0 0 0 would be in the middle of the vessel. The 0 0 1 010 is direction and angle and it's real easy to mess that up, but the 1 in the middle is the facing direction so if you change that to -1 the port will face the stern 0 0 -1 010 just like the bay docks. There are easier ways to do this but it involves downloading a couple of things and I don't want to get into that right now. Maybe another time. It's good to crawl under the hood and do it old school to learn anyway.
And like Jon said this is a Alpha so if you have it you are on your own as we won't give any support on it (too many other irons in the fire) so if you want to change something you are on your own. But this gives one a chance to understand O and the way it works and also get better at modifying it. But I am always willing to give technical advice when I can.
The missiles depend on having the fuel not set to infinite but I didn't know of any problems with them crashing Orbiter.
Two variables are involved here. With limited fuel unchecked and firing them with the stock scn (earth orbit) and they go towards the planet you will most likely ctd. I have never had a problem under the right param's and not near a planet.