This afternoon I was trying different file formats with different ebook readers. This is what I conclude and please help me if I am wrong.
For Kindle you need to get book files in .mobi format, for iPad and Kobo in .epub
first download books in .epub format
then import them to the iTunes library in your PC
then sync the iPad and books will be in the app called iBooks, they work like music
download books in .mobi format
connect kindle to PC
copy books in the folder called documents, if its not in documents it does not show in the kindle library
in the kindle you may also add some music by putting mp3 files in the folder called music (so you can read and listen to music at the same time)
Kindle takes a while to show the books that you put in the documents folder as processor is slow but eventually they show up
download books in .epub format I could not get .mobi format to work well worked poorly PDF is bad for size and pages
connect Kobo to PC
transfer files to anywhere in the Kobo directory.
and yes thank you Calibre is fantastic I am using it now!
then you will also have to wait a while until the books show up and from what I see you have to go more slowly and add book files in small groups or the processing content wheel turns forever and nothing happens.
If you have epub files and want to have the same book in a mobi file go here.