I want to make an universal build, but I create my UI entirely programmatically.
1) Can I add my different view controller classes to the device-specific resources directories? Or must classes be shared along both devices?
2) If I must share the classes along both devices, what's the safest way to conditionally load classA or classB depending on if it's an iPhone or iPad device?
On every view controller you can do a device check to see which device is running your app and accordingly build your UI. ie, use only one set of view controllers and in the *.m files, in an if-else loop, build your UI accordingly.
Refer to this post to do device checks: http://stackoverflow.com/questions/448162/determine-device-iphone-ipod-touch-with-iphone-sdk
PS: In your if-else, do an if(iPad){} else{} check as a best practice, since, often times than not, people forget to check for iPod Touch if they do if(iPhone){}else{}