Questions on automatic backup and missing space on external HD's

First, backing up to an internal drive is a really bad idea. If your computer gets infected with malware, such as one of those that locks all your data until you pay a ransom, you will not be able to access your backup. Or a virus could destroy all your data, including your backup. A hardware malfunction, such as a PSU shorting out and frying everything inside, could also takeout all your data, including the backup drive.

Backups should be kept external and physically connected to your computer only when updating the backup. It isn't as convenient as automatic backups but it's much safer. One way to ensure data is backed up as quickly as possible is to use a good, paid cloud backup service (the free ones have been known to disappear with little or no warning and are rarely secure), such as Carbonite, CrashPlan, or Backblaze, in addition to your external backups. Those work in the background, periodically uploading new and changed data to the service's servers.

For data to be reasonably safe, it should be kept in three physically different places, such as on the computer, on an onsite backup, and on an offsite backup. No matter what medium you have your data on, it is subject to failure, including ones used for backup, hence the need for more than one backup. One of the cloud backup services mentioned earlier can be used as an offsite backup although I prefer to use them to supplement a physical offsite backup.

There are several ways to make backups. The most common are imaging, cloning, folder/file syncing, and just manually dragging or copy/pasting.

Manually copy/pasting or dragging is inefficient and is highly subject to human error. It should only be considered if one has so little data to backup, it could fit onto a small USB flash drives (btw, flash drives aren't all that reliable so extra ones should be kept in case one or more quietly fails). Obviously, this shouldn't be an option for you.

System files (specifically, OS and programs) can't be simply copied and pasted to another drive. The most common ways to back them up is imaging and cloning. Imaging is like taking a photo of your system drive or partitions. The image would be the equivalent of a photo negative. The image would be used to "print" the information in it to restore the original drive or partition or to transfer it to another drive or partition the same as a photo negative is used to make a print. Imaging is the best way to backup System files since images normally get compressed a bit and one can keep multiple images on a single backup drive. The downsides of imaging include not being able to directly access individual files and folders in the image (although some imaging programs allow one to mount an image to access them) and imaging is an inefficient method of backing up data due to the resulting larger size of the image and the amount of time it takes to make an image since each image has to include all the data being backed up in each image. Some imaging programs use incremental or differential imaging to reduce the size of images after the initial image and reduce the time required to make them. However, should any one of the set of images get lost or corrupted, the entire set will be lost or only partially recoverable. It's much safer to make full images.

To facilitate imaging System files, they should be kept on their own drive or partitions, segregated from data files.

Windows Backup and Macrium Reflect Free (here is a good tutorial on how to use Macrium Reflect) are examples of imaging programs. I recommend the latter.

Cloning can be used for backups but is intended for making a duplicate of a drive or partition. It is too inefficient to use for backing up data and should be used only to move the contents of a drive to another drive, such as when upgrading a drive to a newer one. Imaging can be used for that but one would require additional steps (and time) and an intermediary drive to temporarily store the image whereas cloning goes directly from one drive to another.

While imaging is necessary for backing up System files, it is too space hungry and time consuming for backing up data. A more efficient way to backup data is to use a folder/file syncing program such as FreeFileSync or SyncToy. Folder/file syncing programs first examine the drive or folders you have selected to be backed up on the source drive and compares them to what is on the destination drive—the backup drive. It will then copy the files from the source drive to the destination drive and delete files on the destination drives as necessary to make the destination drive essentially an exact copy of the source drive. Since only changed and deleted files are dealt with after the initial backup, backups take far less time, put less wear and tear on the drives, and make a backup that can be used as is or can have files easily read or copied from the backup.

One thing I especially like about FreeFileSync is it has a feature to save files deleted from the backup to a versioning folder or drive so, if you accidentally delete a file or it gets somehow corrupted, you will still be able to recover it. I have a HDD in my computer dedicated to versioning and I also back up that drive.

Something else worth mentioning is that HDDs should not be overfilled. They need at least 10-15% free space at all times to allow for defragging, etc. SSDs should have 20-25% free space for similar reasons.