The order of the columns does not matter. Magmi converts the column name into a column index, then processes the data for those columns row by row.
The skus are used to associate the item in the CSV with an existing item in Magento. Changing the sku in the Magmi datasource would cause that item to be uploaded as a new item.
If you're wanting to change the skus, I would recommend deleting the old items, changing the skus, then uploading the new ones.