The liquid that settles out is usually quite noraml if the tomatoes have a lot of water in them. I have seen this clear liquid being over 3-4 inches with all the red floating at the top. Because I use mostly plum type tomatoes and chose varieties that are meaty with little water, they give me a nice thick sauce. The last couple of years, I also slice them open lengthwise and use my thunb to scoop out most of the seeds and clear liquid from the centers. I use the Roma food strainer on them and get a nice skinless and seedless sauce. Pressure canning is usually a bit faster process compared to a water bath. I do hope you added the citric or other acid.