Like in Windows, we mostly use two drives one to install windows and other to save important data so that if windows crash, our data is saved.

So, where to store data in linux so that it is safe, if in case linux crashes and re-installation is required.

In linux, you can use LVM (or Logical Volume Management) store all the files in your /home directory, if you prefer to simply use seperate partitions, you can do that too. If you have extra hardisks, Linux supports software RAID, to ensure data would survive a disk failure as well.

http://tldp.org/HOWTO/LVM-HOWTO/benefitsoflvmsmall.html
http://tldp.org/HOWTO/Software-RAID-HOWTO.html

I notice you are trying to apply your fears, uncertainties and doubts regarding the Other Operating System to Linux. Linux is not Windows and in more than one aspect. When it does crash it doesn't bring down the whole system like Windows does. If your browser crashes you still have your Desktop Environment. If your Desktop Environment crashes you still have all services running. If one of the services crashes it doesn't necessarily affect others. Only when the kernel can't deal with things (hardware instability, overclocking, unstable software or avoidable configuration settings, driver or kernel development, exposed vulnerabilities or any OOPSes caused by the alignment of your machine with Mars and Giedi Prime) you may suffer data loss as a result of a total system crash.


On your external backup media and by using a verifiable, usable backup scheme.
Only when you need to recover from (or cannot afford) data loss you will realize if it is a general misconception that LVM or RAID act as safety nets or not.

We still use tape backups made remotely and stored in a fire resistant container. Sometimes we make the tape locally and then move it.

If you want the same setup as in Windows, you can use your second disk for data (my documents) and mount it on /home.

Having said that, if your second HD crashes or if user mistakes happen, you may assume that with both Windows and Linux your data is lost. So backups are important.