Your applications are in your root Applications folder and will be available to all users (there are ways around that but I wouldn't try it). And you're going about merging your data just fine - just wait until you have all of the data in the account you want to keep before deleting the no longer needed accounts.
What applications do you want to prevent other users from using? Or am I reading your message wrong?
Applications folder is a global access folder for all users on the machine.
If the program was a standalone and in a user account folder, then when you delete that account, so will the app go with it.
So just make sure all apps are in the Applications folder.
You should clone the entire OS X volume first to a external drive, this way in case a screw up occurs you can restore the bootable clone.