Well, then, if I understand you have Mac drive with more than one partition on it that you need to backup to the external drive. You will need to initially partition the external drive using GUID with each partition formatted Mac OS Extended, Journaled. You then want to clone each partition on the main drive to a corresponding partition on the backup drive. The basics are:
A.
Repairing the specific volume and permissions
Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.
Repeat the above for each partition you will be backing up. Permissions repair is only needed for a partition on which you have OS X installed. If you have different versions of OS X (say Tiger and Leopard) then you need to repair permissions using Disk Utility while booted into each respective OS version.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
B.
Clone using Restore Option of Disk Utility
1. Open Disk Utility from the Utilities folder.
2. Select the
destination volume from the left side list.
3. Click on the Erase tab in the DU main window. Set the format type to Mac OS Extended (journaled, if available) and click on the Erase button. This step can be skipped if the destination has already been freshly erased.
4. Click on the Restore tab in the DU main window.
5. Select the
destination volume from the left side list and drag it to the Destination entry field.
6. Select the
source volume from the left side list and drag it to the Source entry field.
7. Double-check you got it right, then click on the Restore button.
Destination means the partition on the external backup drive.
Source means the partition on the internal drive.
Does this answer you question?