The factory numbers help differentiate between the design generations of a specific model, for instance the 986, 987, and 981 are all Boxsters. But to differentiate, the first generation (1997-2004) is the 986, the second generation (2005-2012) is the 987, and the third generation (2012+) is the 981.
This is the same system used for all of the Porsche models. However, the 911 is confusing, because the name '911' is the model name, like Boxster, not the factory number. The factory numbers of the 911 have varied with the design generations. The very first '911' had the factory number 911, then later iterations have had the factory numbers: 964, 993, 996, 997, and 991.
Carrera is often confused to be interchangeable with the model name 911, however it is actually a subset of the model. You can purchase different models of the 911, such as the Carrera, GT3, GT2, Carrera 4, Turbo, Turbo S, etc. Which is like the difference between a Boxster, Boxster S, and Boxster Spyder.
Hope that helps clarify!
EDIT: Take a look at the RennTech forum, they breakdown their sub-forums by the number designations.