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There isn't a setting found in the Preferences window to change this. I suggest checking your IIF file, and make necessary changes so your checks get imported with numbers on them.
You can take a look at the sample files of this article: IIF Overview: import kit, sample files, and headers. You can reference the sample files to ensure your format is correct.
Learn more of what you can do with IIF files by opening this article: Tasks you can do with IIF files.
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