While the iPad is sure to make a splash I'd not count on it to become the overwhelming market share leader.
ePub, the open standard, is the "tide", as it were. Closed system approaches (Kindle/iPad) are the waves (alibet, large at times).
With that said & noting that my opinion and several dollars will get you some coffee at Starbucks, I'd suggest that you look at providing eBooks to Kindle and Sony eBook readers first.
Having InDesign, you can publish output for Kindle almost immediately.
Keep in mind that, in North America, Kindle has the dominant market share; this makes eBooks for Kindle a "bird in hand".
iPad is the "bird in the bush" just now. Why wait for whatever may/maynot happen with it?
Visit this page in Adobe's web space:
Download and read the Whitepaper.
Obtain Calibre. Become comfortable with the work flow. Then publish for Kindle.
Next, look over the formats supported by Sony's eBook reader.
Again, with the Adobe products you have on hand, you are staged to publish to this market.
Remember, both Kindle and Sony are "birds in hand".
I'd suggest establishing a presence with each of these.
Let things settle out with the iPad. Look closely at what Apple will/will not support.
How "captive" will you be if you go for whatever the iPad market *might* be.
While I'm not looking to get into the "publishing biz" I do have an interest in how to share topics I'm interested in with others and eBooks is, clearly, an excellent venue. To date, it looks to me that Sony is the most versatile (format support), Kindle is widely used/supported and getting into Kindle format is not so hard (via InDesign/Calibre), and iPad is still an unknown (marketing talk has little meaning - run time has meaning). Again, what is significant about the Sony (and others) is the support for ePub.
A final observation. If not already done, consider getting yourself in the current CS4 applications (with, of course consequence updates).
The most current InDesign release is much better for support of eBook publishing.
As to your question: submitting to Apple for iPad -- that's something you will have to ask of Apple if you want the "straight up" of it.