I have been building a single page app using requireJS and so far loving it. I have come to the point of developing other parts of the site outside of the main app and am not re
So require.js should always be used on any page to allow for modularity and a clean namespace. I believe each 'app' needs it's own main.js script. When optimizing your site r.js allows for you to exclude modules from the compilation which you should do for jQuery always.
That way require.js will always load jquery.js on the fly and most of the time from the cache. Finding other modules that might be cached between your app and homepage will have to be done at your own discretion and depends on the flow of your users and other factors.
It sounds like you have two projects, an app and a marketing site. I believe those should be separated to quite an extend and should have their own respective 'js' folders containing their own main.js.