You do not need to empty the database with each import. Magmi has the ability to update products on the fly without deleting them first.
If your concern is removing products that are no longer in the CSV, you can use a plugin I wrote and posted on StackOverflow here: https://stackoverflow.com/a/18447266/1332068
The indexer issue has also been asked about and answered on this site as well.
https://stackoverflow.com/a/19384326/1332068
I urge you to search thoroughly before asking questions as there are several solutions already available for Magmi on this site.