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I'd imagine you'd want to remove the seeds unless you won't mind their texture in your sauce. after you've pureed it, you can push it through a sieve, if you have one of those. Or, can you try scooping them out of the whole canned tomatoes?
Unless you really hate the seeds, you should be ok with any recipe that calls for crushed/pureed tomatoes. I don't find that the tomato seeds affect any tomato sauce that I make.