As in iOS, you can organize your Launchpad icons as you please using drag-and-drop. You can reorder apps, move them from one page to another, and even put them in iOS-like folders. Note that Launchpad folders are entirely independent from the /Applications hierarchy: creating a folder in Launchpad won't create a folder in /Applications, for example.
Your problem seems to be related to the fact that you've got so many apps. Again like iOS, there seems to be a maximum on the number of pages of apps Launchpad can handle. If you really need all 400+ apps on your Launchpad, there's not much you can do other than reorganize everything into folders to free up some slots. But I doubt you need instant access to everything Adobe has ever installed on your computer, so you have a few more options to clean out your Launchpad:
- Delete apps entirely. There's probably a few apps on your computer that are just sitting there, never to be used; you can free up space on your Launchpad and on your hard drive by getting rid of them.
- Apps from the App Store can be uninstalled directly from Launchpad by holding option/alt and clicking on the black X over the app's icon.
- Any app can be deleted by dragging it from the Finder to the Trash.
- Alternately, you can use something like AppZapper to delete an app along with any hidden auxiliary files.
- Move apps out of Launchpad's sight. Launchpad looks for apps in /Applications, /Developer, and ~/Applications. If you like those folders to be as pristine as your Launchpad, you can move your extraneous applications to a different folder. Launchpad will lose track of them as of the next reboot.
- Just remove the Launchpad icons. Finally, Andreas Ganske has developed a preference pane which modifies the Launchpad database to show or hide whatever applications you want.
If you just want a clean Launchpad, option three is probably your best and easiest answer. Options one and two are there if you like to keep your /Applications folder clean, too: useless apps might as well be deleted, and your CS4 uninstallers could probably be moved somewhere a little more out of the way until you need them.
Finally, you hint at having problems with having Launchpad duplicates. As I mentioned in an answer to this question, this may be a problem of actually having more than one copy of the same app installed.
Hope this helps clear up some of your upgrade troubles!