Its the same as how we did it before iTunes 11, where you open apps and drag them, and then sync. If you can't find the location using the new iTunes 11, you can add the side bar back that used to be on the old version. Pull down "view" and click "show sidebar". Now iTunes 11 will act like iTunes 10.
Now, if you never did it on your computer before, even in an older version, that's a different issue, and basically, (using the sidebar), click on the name of your device, for example "iPhone", and when you do a screen comes up with a bunch of buttons on top. On the left you'll see "Summary". A couple over, you'll see "Apps". Click on Apps. Now you'll see a screen with your phone's current app organization, and a scrollable set of screens on the side. You can scroll through and see all your iPhone's screens. You can organize by dragging and dropping, until you have it the way you want it. Then, once you are done, there's a sync button at the bottom right. Push that, and the computer will begin to process the changes to your iPhone.
By the way, if its your first time, when you organize, you can also make folders to group apps to help with organization. You just drag an app over another and it will make one. You name the folder, and then you simply drag the other apps you want in the same folder.
Sorry if this is something you already know, but I noticed no one answered your question, and thought I'd try.