First the books must be unprotected (no DRM) ePub or PDF files for you to import them into iBooks. The files must have the right suffixes. If they are compressed as zip files, then you'd need to download them in an app that can uncompress them first.
If the downloaded books won't Open In iBooks from Safari, try using GoodReader (if you have it) to go to the site and download them. Then use Open In to copy them to iBooks. There are other options. You could even let them go into your Vault app and see if you can use Open In to copy them to iBooks from there.
I don't use SmashWords, so I can't be more specific. Sorry.