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1. Epub is the preferred format for most iOS reader apps. However it would help if you specified what reader you were using. iBooks? Stanza? BlueFire? GoodReader? Sideloading Kindle? Since you didn't specify, I'll assume iBooks, but just be aware that there are more (and much, much better) readers on iPad than just iBooks.
2. If your target is iBooks, you can use Calibre's built-in "Connect to iTunes" option (in the Connect/Share toolbar dropdown). If your target is Stanza, it's best IMHO to use the Calibre content server and download books from within Stanza or you can drag and drop in iTunes via the app tray. If you're using Bluefire, you can navigate to bluefirereader://nav/transfer in Safari on your device and follow the on-screen instructions or you can drag and drop via itunes like Stanza. If you're side-loading Kindle, you probably need to jailbreak your device or google for it.
3. What do you mean "retain your metadata"? Are you using Calibre to organize your book collection, or just to convert formats? Anyway, I think the answer is to use Connect to iTunes to sync to iBooks or use the content server from reader apps that support it. If you have to manually drag the files into iTunes yourself, I guess you lose data?
4. Edit the book's entry in Calibre and delete the formats you don't need from the list in the top right. But why would you want to do that? Ebooks are cheap storage-space-wise, and it's a good idea to keep the original around in case you ever need to convert from it again.
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