OS X installation on external HDD I am planning to install a second OS X on an external HDD, I was wondering when I boot in external HDD will it in any ways affect my first OS X installation? Will it have the permissions to write or read from it? Or will spotlight start to index that HDD? If yes how can I isolate my first installation from being affected? (without using third-party apps or FileVault)
The disk which you don't boot on will show as an external drive to your current OS HD. You'll have full read/write accesss, Spotlight will start indexing it.

To prevent Spotlight from indexing your second drive, open a Terminal window and type: 
    sudo mdutil -i off /Volumes/2NDDRIVENAME

and replace "2NDDRIVENAME" by the name of the disk you want to exclude. Beware if you have a space in the drive name, you may need to use the "\" escape character:

sudo mdutil -i off /Volumes/MacHD

sudo mdutil -i off /Volumes/Macintosh\ HD