You have good reason to be a little bit confused. Let's see if I can shed any light on it at all:
First, the source of some of the confusion: There are
two jurisdictions on the mountain, one state, and one federal. If you camp in the area controlled by the US Forest Service, they do things by zone. If you camp in the area controlled by the California State Park Service, you must camp in a specific camp. If you do some kind of a loop that takes you through both areas, you must have an overnight permit from the agency that controls where you plan to camp. If you're "just a passin' through" (i.e. you won't camp overnight in a given area) both agencies accept the other agency's permit.
This map shows the overall areas fairly clearly and shows the camps (all four of them)

for the state portion of the wilderness.
For the Federal portion, you must select a zone. You may camp anywhere within that zone provided that you meet certain requirements -- see the pdf link below for the requirements.
San Jacinto Wilderness Zones
Map of zones:
http://www.fsva.org/pdf/WildernessMap_2007%20II.pdf
Chinquapin Zone
The best camping area in this zone is along Chinquapin Flats Trail — Pacific Crest Trail about a quarter mile south of Saddle Junction. The closest water is in Skunk Cabbage. Zone capacity is 75.
Skunk Cabbage Zone
This is the most used and, consequently, the most abused area in the wilderness. Camping is not allowed in the meadow because the ecosystem is extremely fragile. Water is available at the north end of Skunk Cabbage Meadow and at Willow Creek. Zone capacity is 75.
Tahquitz Zone
Easy access, lots of water and lush vegetation make this zone very popular. Water is available almost year-round in this zone. Zone capacity is 50.
North Rim Zone
Although this zone covers a large area, there are few suitable camping areas because of its steep terrain. Because of erosion problems, camping is not allowed at Willow Creek Crossing. Water is available in this zone. Zone capacity is 75.
Lower Basin Zone
A lot of beautiful camping areas are on the large plateau in this zone. During the summer, the water does not flow freely and, consequently, the area’s popularity drops. Zone capacity is 75.
Desert View Zone
This zone is located at the southernmost end of the wilderness. The vegetation varies from coniferous to high chaparral and scrub brush. Very little water is in this zone. Zone capacity is 50.
OK, so clear as mud?
Hope that helps,
HJ