There are a couple options that I've used:
1) You can add template files, such as a cover page, into the sigil folder. When you click to add a cover, it will automatically use that template cover.
2) You can create a blank epub with all the files you wish already setup (like your template file), then create a shortcut to that file. Use the shortcut to open Sigil, then "Save As" to give it a new name without changing the template.
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