You know, with the quality artwork that's a part of this comic, plus the fantastic supporting material he has in his extras, you could easily set up markers using printouts of images of the craft. Deciding on the scale of your tabletop would be more difficult, as the comic is generally vague on acceleration and such of the ships involved. The problem with futuristic combat is that the top-line combat aircraft of today already engage their targets "over the horizon" (that is, beyond visual range of human eyesight) the only time aircraft dogfight eyeball-to-eyeball is when there's a requirement of confirming the nature of the target (i.e. make sure it's not a civilian plane in the wrong place at the wrong time) And in space it's really hard to disguise your heat signature, much less the emissions of a nuclear reactor. Stealth isn't really an option in space, so you either find something even more "noisy" to hide yourself in, or make darn sure nobody with big guns gets close enough to use them.
I know that from a story point of view it's not something we'd want to read about, but the U.S. military is trying really hard to develop drones able to operate autonomously, recognize profiles of known enemy craft/vehicles, etc. These are inevitable, and we as SciFi fans have to recognize that, unfortunately, the human will be the "great wizard" in the background sending out the mechanicals to do the ugly part. Machines are alot cheaper than people. Now that said, I don't see computers getting smart enough to fully replace us. I do see, however, drones that are basically sensor-platforms being launched from fighters. Small and fast, they close in and locate/ID the exact nature of the targets. They're expendable, so you don't care if they emit lots of EM noise. In fact, while your enemy is blasting them, you've got more information on their weapons. Now you have more details on the profile, you feed that to your missiles and launch. While the enemy is dealing with that problem, you close in even more, and keep hitting him with as many missiles and such as you can. You want to hurt him before he can hurt you.
Think of submarine warfare: torpedos can self-target using sonar, and aircraft drop sonar buoys to locate submarines so that the ships don't have to use active sonar, but rely on someone else to announce their location and then get shot at for it.
Sorry, this has gotten rather long, but it's my take on a table-top of space warfare.