By default VDub splits only on keyframes which, typically, are 10 seconds apart. If you can figure out how to Smart Render, then you can split by a specific frame and only the rest of that particular keyframe gets reencoded.
The problem with the subs is that they keep the same timings as originally. If each episode is, for example, 25 minutes long, the first episode's subs begin at the zero mark and are included. The subs for the second episode begin at the 25 minute mark and don't begin until after the episode is over. And so on. The subs for the second and subsequent episodes must be (negatively) delayed by an amount equal to the total time of the episodes that went before. Once you have that taken care of, you can add them into AutoGK using the CTRL-F8 trick.