Languages used in India are usually not well supported on ePub readers. In particular, the display of vowel signs causes problems.
Generally speaking, the following approach should theoretically work:
1. Convert your source text to Unicode text or html files.
2. Create a new ePub with
Sigl, add your source files to the project and format them or convert your source files with
Calibre.
3. If the iPad fonts don't support Kannada, also embed a free Kannada font in your ePub.
4. Test your ePub on your device. Make sure that all vowel signs are correctly rendered.
I created a quick and dirty Kannada epub from a random newspaper article. If it displays fine on your iPad, you can use it as a template; if it doesn't, the iPad most llikely doesn't support Kannada in ePubs.