Backup/restore does NOT copy third party applications.
If you're going to have both devices on hand at the same time, use the Switch device wizard.
If not, run the backup as you normally would. This will backup all of your data/settings (not your third party applications).
To back up your third party applications, follow these steps: How do I backup my Third Party Applications on my BB? - BlackBerryFAQ
Once you receive the new device, restore your backup file to get your data/settings on the new device. Then follow the steps in the link I provided above to restore your third party applications.