vugtitan
This will all become clearer to you once you receive your Kindle. You can experiment and try to move books between your Kindle and the various apps and see what happens.
If you're really concerned about indexing you can add your books in the evening before you go to bed. Make sure your Kindle in connected to power and let it index overnight. My understanding that you shouldn't add more than a couple of hundred books at a time as the time to index will vary based upon how many books you add.
I don't keep a lot of books on my Kindle at one time, so indexing hasn't really been an issue for me.