Q: will choosing the manually back up option in iTunes save everything that is on my iPhone to my computer? Including app data

Hello CallRinny,

I understand that you have a question about your backups to iTunes and which one you should use. Let's go over what that covers. 

Typically an iTunes backup will cover just about everything on your iPhone. The best thing to look over is what doesn't iTunes back up and what the encrypted backup covers. Take a look at the information below to clear this up. I would also make sure that the apps are saved to your iTunes library so when you restore from your backup, the apps will sync back over in one sitting instead of downloading them from the App Store. 

About backups in iCloud and iTunes
https://support.apple.com/en-us/HT204136
 

iTunes backups

From your Mac or PC, you can make a backup of your device in iTunes. Syncing your device with your computer isn't the same as making a backup.

An iTunes backup includes nearly all of your device's data and settings. An iTunes backup doesn't include:

• Content from the iTunes and App Stores, or PDFs downloaded directly to iBooks (You can back up this content using Transfer Purchases in iTunes.)
• Content synced from iTunes, like imported MP3s or CDs, videos, books, and photos
• Photos already stored in the cloud, like My Photo Stream, and iCloud Photo Library
• Touch ID settings
• Apple Pay information and settings
• Activity, Health, and Keychain data (To back up this content, you'll need to use Encrypted Backup in iTunes.)

Learn how to make backups in iTunes, how to find them on your Mac or PC, and how to delete backups you no longer need.

Let me know if this clears this up for you. 

Take care 

Hey CallRinny,

To get your apps, you would need to download them from the App Store section in iTunes. The link below will walk you through how to download anything that was previously purchased to have it locally saved in iTunes. 

Download your past purchases
https://support.apple.com/en-us/HT201272

Take it easy

Hi CallRinny,

It was not problem with the assist. 

Have a good day