Choose File | Import | Account Budgets and set up a template of the fields you want to import. Generally you need a spreadsheet containing a row for each account-department and the amounts for each period (12 or 13) in your fiscal calendar. If you budget annually, then you'd probably want to divide the annual evenly amount by 12 to create the 12 budget buckets.
There is a spreadsheet GLBUDGIM.XLS in the sample data (normally installed in \softrak\Ledger\samdata).
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Andrew Bates