I have a laptop and the hard disk is divided to system partition with Windows 7, and another partition for storage. Both partitions are encrypted with TrueCrypt. I attached a second hard disk on the place of the cd rom and i want to install debian on it and have dual boot. Will this break the encryption of the system partition or messed up the boot sector?
That shouldn't break encryption. However, dual boot with TrueCrypt/Windows (especially with multiple encrypted partitions) and Debian might be a bit iffy. In terms of systems overwriting each other's boot information, I mean. But it's been a long time since I messed with that stuff, and maybe it's been sorted. Perhaps others can provide clearer guidance. But whatever you do, make sure that you have usable backups for everything, before you get into it.
One sure fire way to accomplish this and keep yourself safe as can be: disconnect the original hard drive while you create the second new drive AND while you are creating the debian system I advise you to place the /boot files (that is what starts linux) on a USB stick. When you want to mount the debian system you would simply insert the USB and when you power on the machine, if its usb bootable of course, you will be presented with your password prompt. My linux machines are all 100% encrypted via LUKS, but you would not have to encrypt since you are just starting out. I would, but you don't have to. Two keys to this approach would be no "marks" on the original hard drive, and "bad guys" can't infect the /boot files since you would pull the stick out after mounting the machine. Its safe and easy to do, at least after doing more than a dozen of them.
Can i backup the boot sector of the first hard disk so if something goes wrong i can restore it later on?
Even without doing the second drive you should ALWAYS have a copy of the MBR. Its simple to make. BTW - the TC rescue disk and you should always have one already contains the backup needed. Still I keep dd copies of my MBR's for every single device I use encryption on. Things happen and a saved MBR (this includes the essential partition table within it) can save your bacon if something gets overwritten.
