How will you going to architect your project ?

• when you compile the project Titanium converts your javascript code and gets interpreted.http://stackoverflow.com/questions/2444001/how-does-appcelerator-titanium-mobile-work 
• The code present in the Resource folder gets compiled. when you build for iOS then all the code present in your Resource apart form android folder gets compiled. and when you build for android then apart from your iphone folder all gets compiled.
• When you compile for android your app will run on android devices and for iOS build it will run on iOS devices. if you want to know under the hood then visit this linkhttp://titaniumninja.com/post/10559549700/fastdev-for-ios-how-it-works/