There are two approaches to handling screen size restrictions when building your application.
Lowest Common Screen Size: Build to whatever the smallest screen is your users are likely to encounter. If you have some users on old iPads then you might be stuck with 1024 x 680. This way everybody can see the content, though those on bigger screens will have a worse experience
Allow some scrolling: Build your application to the most common screen size, allowing for some scrolling for those on smaller screens. Ideally this should be vertical scrolling only as this is a common experience. Horizontal scrolling is not good design and scrolling in both directions is a complete mess.
A final consideration is to design for a specific screen ratio, so 16:9 is very common at the moment, though 4:3 appears on iPads and some other devices. This allows the users to zoom the view if required and get a full screen experience.
If they are using mobile phones then it is probably best to design a distinct application as user interfaces are very different on these devices.