Here are my settings - stick with these and you will have something up and running. I like to see collections by author, with the ability to sort by title within an author collection to see a series in order. Since it sounds like you have deleted your device contents a few times, your best bet is to just start from fresh (all your books you want kept are already in calibre, right?).
- Plug in your Kindle.
- Choose "Customise Kindle Collections".
- Make sure the *only* dropdown that is set to "Create" is for "Author Sort".
- On that row, set the Prefix to ~ and optionally the Suffix to ~ (if you are OCD like me and want to see ~Cussler, Clive~ as the collection name). Set the Minimum to one.
- Make sure all the checkboxes down the bottom are ticked, and click OK.
- Go to Preferences -> Metadata plugboards. Create a plugboard for mobi, device Kindle2 and set the template to:
{series:|| }{series_index:0>2s|[|] - }{title}
- Set the destination field to title and click Save plugboard.
Now you have everything configured. Select the books you want on your Kindle (just pick a few to begin with), right-click and choose Send to Device to send them to your Kindle. Now you have books on there that will have been internally renamed thanks to the metadata plugboard when the Kindle looks at them.
Now you want to create your collections. Just click on the main Kindle Collections button, or choose "Create collections on the Kindle from Calibre" from the dropdown. It will take a moment or two, and when done produce a report telling you what collections it has.
Choose Eject from the Device menu, and unplug your Kindle. Hit Home, Menu, Settings, Menu, Restart. Wait a minute or two for your Kindle to reboot. Wait a few more seconds for the count of collections to settle.
On your home screen, make sure the sort is set to sort by "Title". Since we prefixed the collections per author with ~ above, that will sort them at the top. You should see a collection for each author (assuming your author column in calibre is propulated correctly).
Click on one of those author collections. Set the sort to by "Title" and you should see a series listed in incremental order, thanks to the metadata plugboard.
All this setup is a one-off thing. The next time you want more books on there (or remove some), just plugin in your Kindle, add/remove the books, click on the Kindle Collections button on your toolbar, wait for the report, and follow the eject and restart steps.