Core allows you to specify the invoice templates you want for a different project or contract types at the global level and project level. It has the default templates pre-selected, but you can change them if needed. You can also overwrite these templates at the invoice level temporarily. Check the Core Help for details.
You can also have BQE Software create custom invoices for your company and add them to your Core database. Then you can select them as your default templates instead of the standard ones available.