Read this article (follow link) for a more in depth understanding of canning tomatoes.

Canning Tomato Products
Following are general instructions for canning tomato products, including selection, acidification, and preparation and processing.

Selection
Select only disease-free, preferably vine-ripened, firm fruit for canning. Do not can tomatoes from dead or dying vines. Unripe tomatoes are more acidic than ripened fruit and can be canned safely with any of the following recommendations. Treat all ripe tomatoes (yellow, green, pink, orange, red, etc.) the same.

Acidification
To ensure safe acidity in whole, crushed, or juiced tomatoes use the following recommendations.
Acid                                         Pint                                        Quart
Bottled lemon juice       1 Tablespoon                          2 Tablespoons
Citric acid                         1/4 teaspoon                          1/2 teaspoon
Vinegar                             2 Tablespoons                        4 Tablespoons

Add acid directly to the jars before filling with product. If desired, add up to 1 Tablespoon of sugar per quart to offset acid taste. Vinegar may cause undesirable flavor changes.

Sodium
The use of salt is optional in all canned tomato products. Salt is used in canning only for flavor or color protection.

What causes tomato juice to separate in the jar?
Liquid at the top and solids at the bottom indicates that the juice was made prior to heating (perhaps run through the steamer, sieve, or food mill raw). The enzyme that causes separation is activated by exposure to air and inactivated by heat. Leave tomatoes whole or in large chunks (do not chop). Heat before juicing to minimize separation.
Liquid at the bottom and solids at the top indicates too much preheating (more than 5 minutes). Pectin breaks down when overheated and separation results. If separation occurs, shake the jar before opening.

 RECIPES
Tomato Sauce

• 5 pounds tomatoes

• 1/2 cup chopped onions

• 3-5 cloves garlic, minced

• 1 teaspoon salt
• 1 teaspoon oregano
• 2 teaspoons minced basil or six whole leaves
• 1/8 teaspoons black pepper
• 2 teaspoons brown sugar
• 2 teaspoons vegetable or olive oil

Yields 4 pints 

1. Wash tomatoes, and trim off bruised or discolored portions.
2. Chop onions and garlic. Set aside.
3. Dip in boiling water for 15 to 30 seconds or until skins split. Dip in cold water and slip off skins. Remove cores and quarter tomatoes. (Skip this step if using the sauce mill or food mill.)
4. To prevent juice from separating, quickly cut about 1 pound of fruit into quarters and put directly into saucepan. Heat immediately to boiling while crushing. Continue to add and crush freshly cut tomato quarters to the boiling mixture. Make sure the mixture boils constantly and vigorously while you add the remaining tomatoes. 
5. Boil 20 minutes, uncovered, in large saucepan. Put through food mill or sieve. 
6. Saute onions and garlic in olive oil until tender.
7. Combine sauteed vegetables and tomatoes and add remainder of spices, salt, and sugar. Bring to a boil. 
8. Simmer, uncovered, until thick enough for serving. The initial volume should have been reduced by nearly one-half. Stir frequently to avoid burning.
9. Sterilize jars and lids.
10. Acidify (see acidification directions above).
11. Fill jars, leaving 1/2-inch headspace. 
12. Adjust lids and process pint jars for 35 minutes and quart jars 40 minutes in boiling water.

References
Complete Guide to Home Canning. United States Department of Agriculture, Agriculture Information Bulletin No. 539.