You can and you can't. Confusing?
Of course it is.
Heres how to (sort of) do it:
Keynote iOS can grab a regular keynote file via iTunes syncing in the special "File Sharing" section of the Apps tab. In order to create a custom theme you first must author it inside regular Keynote. Once it's finished you can then create a mock presentation using the new theme using one of each of the masters as one regular slide. You don't have to put in any content, just make sure you have 1 slide per master in your presentation. Save the .key file and then move it to your iOS device and open up in iOS Keynote. You can simply copy the blank presentation to start a new fresh presentation without changing the original and it will contain all the slides as masters for your new presentation. You have no access to customizing masters at all in iOS Keynote so you can only change and copy regular slides in order to grow your slide show. You just copy slides to make more if needed of any type of layout.
Make sense? Hope that helped.
- Todd Siechen
Is this really the only way we can do this still? This is horrid and significantly reduces the usefulness of the iPad. This makes creating Keynote presentations on the iPad cumbersome and complicated instead of simple and easy.
Wow Apple, amazing how you can do SO GREAT at so many things and completely blow it on things like this.