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It depends on your preferences, but I'm of the opinion that you can totally use them as is without putting them through a food mill. However, the texture will be more rustic. I often make sauce with home canned tomatoes -- seeds and all!
You can certainly eat the seeds. Did you try to remove most of the seeds when you canned them? Just cut in half anf use your fingers to remove the seeds. you won't get all of them, but you'll get most.