It seems that in the future, we can just use the non-beta iPhone SDK to develop for both at once.
But for now, the only way to develop for iPad seems to be to use the SDK 3.2 beta. However, if I install that, Apple clearly states I should not submit apps to the app store with it.
I'm an independent, one-machine developer. Is there a way I can continue to upgrade my existing iPhone apps while still developing for iPad?
The Best way to do this is to install the 3.2 SDK beta in a location other than '/Developer'. On the 'Custom Install on Macintosh HD', select 'Other' from the Popup button, and point the installation to somewhere like: '/Developer-Beta'.
You can then run Xcode from /Developer/Applications for your iPhone apps, and Xcode from /Developer-Beta/Applications for your iPad apps.
If I'm reading the agreement correctly, the ban on submitting apps with the 3.2 beta applies only to the SDK, not the tools. If you set your app's base SDK to an SDK earlier than 3.2 (which it probably already is anyway), you can then build with the 3.1 and earlier SDKs by selecting them from the "Overview" menu in Xcode.
I've submitted updates to my iPhone apps built with the 3.0 SDK by the 3.2 beta tools, and they were accepted with no issue. As long as you aren't building on the actual new SDK, you should be fine.
EDIT: I don't work for Apple, I am not a lawyer, blah-blah. But it's worked for me, and the warning only specifies the "iPhone SDK 3.2". The Xcode tools aren't mentioned.