I would like to make homemade Ketchup, how do I prepare the tomato?
You will want to remove the skins. Make a small cut on the bottom of the tomato and then drop into a pot of boiling water for 30-60 seconds. When the small cut expands to a large split, remove from the pot and drop into ice water. The skins will slide right off.

You will also want to remove the seeds. You can do this by cutting the tomato and digging them out with your finger. Cook and process as usual. You can "cook the tar" out of the tomatoes until they completely break down into nothingness leaving a ketchup like substance,.

+OR+ you can cooked mixture with whole unpeeled/seeded tomatoes, THEN through a food mill or press through a fine mesh sieve. A food mill and sieve should also catch any seeds and skins.

Edited to clarify.