you are mixing two topics together:
- filesystem/data backup
- software and system management
for the first part of your question the most common answer in this case is relatively simple and i can suggest to create one or more mount point in different volumes or filesystem partitions as you like. The standard installation profile for Ubuntu provide only a root partition plus a swap space, so when you follow the standard installation wizard you obtain your operative system that uses a total of 2 partition; a better approach can consist in the creation of a third mount point for /home, so all your personal data are stored in a separate disk or in a separate partition, you can do this for all your mount point and you can connect this mount point as you wish, to every and each one hdd in your system or in a separate portion of your hdd. The basic concepts are fairly simple, take a look at docs like this one https://help.ubuntu.com/community/AutomaticallyMountPartitions about fstab and the various mount options .
the answer to the second part of your question is more complex and involves a deep knowledge about both software and hardware and is pratically impossible to give a specific answer to a question so generic. For example, there is no "standard" approach for a system failure caused by a bad video driver, you have to investigate the failure or you have to know how your software and your hardware works to do the right thing to do.