jonjay -
Sorry I didn't see your post earlier.
Anaerobic capacity (CP and glycolytic capacity)is developed through high intensity intermittent training. For CP development, run short but very fast reps with sufficient recovery to keep the intensity and speed high on subsequent repetitions. For glycoltic training, run medium-length reps at high speeds with fairly long recoveries. The goal is to keep the speed high during each rep. If you can't keep the speed high it means you need more recovery time, and it probably means you need higher aerobic power/capacity. The better your aerobic power the more fast reps you can run during "anaerobic" training.
Note that "anaerobic" is not the best term to use, from a technical standpoint, but most people understand that it means generating ATP (adenosine triphosphate) to do work without using oxygen in the chemical processes. Further, not that it's almost impossible to do any work without using oxygen. Even very short reps require oxygen use. There is a constant mixing and blending of the "anaerobic" and aerobic processes to generate ATP.
Now, to answer you other question. Why would aerobic capacity go down while training fast "anaerobic" reps? The reason would be neglect. If you aren't reduce the amount and type of training that develops aerobic capacity/power in liue of "anaerobic" training; you will lose aerobic ability. Runners who include both aerobic conditioning and "anaerobic" conditioning will have the best of both worlds.
Remember, as you strive to learn about training and physiology that many terms are thrown around in dicussions. Don't let the various terms persuade become more important than the training you perform to "get in racing shape." It doesn't matter if you call a workout anaerobic capacity or glycolytic capacity training. What matters is you do the training that develops your racing fitness/performance capacity. Some of the best training you can devise might not have a name for it - at least you might not know what it woud be called. I used to run a hard, hilly 8 miler when I was in my late teens. I didn't have a name for it. Now I might call ita a tempo run. Not knowing the name of the type of run didn't mean I wasn't getting the effect I needed to race well. Keep it simple!
Good luck!
Tinman