There's a lot of work that goes into theming an app (or the iPad as a whole, for that matter). All I can suggest is that you take a look at the specific images within the app itself and theme those.
You can look at the images by using something like iFile (the app will be at location /var/mobile/Applications). Once you find the images you want to theme, either make your own theme or modify an existing one.
In addition to the images within the specific app, there are also the images for the iPad itself that are used by the app (and are themed for overall use). For example, most apps use the images for the status bar - so if you want to change that within the app, you'll have to locate the system image. Then, if you change a system image, it will be changed throughout the iPad, not just within the app you're theming.
I'm not trying to discourage you, but it really does take trial and error. Which is why I usually get a theme from Cydia - the developer already has done all the hard work.
Then, I modify little bit and pieces here and there to make it "just right" for me. So, really, it all depends on how much digging around you wish to do.
Marilyn
