Unlike a water bath canner, the jars do not need to be completely covered with water. The directions that came with the pressure canner tell you how many cups of water to add in order for it to generate the right amount of pressure. You vent the pressure canner a considerable length of time while the water boils (with the jars in and the lid on). This causes steam to push out all the air. So the jars are in a space filled with only boiling water and steam. In theory, both will have the same temperature, which will be 240 F, substantially high than 212 F of an open water bath canner, due to the increased pressure. And since there is no air, just water vapor, the heat will be easily conducted to all sides of the jars.
If you want to can low-acid foods such as red meats, sea food, poultry, milk, and all fresh vegetables with the exception of most tomatoes, you will need a pressure canners. These foods fit into the low acid group since they have an acidity, or pH level, of 4.6 or greater. The temperature which must be reached and maintained (for a specified amount of time) to kill the bacteria is 240 F. Pressure canning is the only canning method recommended safe by the U.S.D.A. for low-acid foods such as vegetables, meats, and fish. Ordinary water bath canners can only reach 212 F and cannot to kill the types of bacteria that will grow in low acid foods. This temperature can be reached only by creating steam under pressure as achieved in quality pressure canners.
To learn more: Pressure Canners at pickyourown.org