When partitioning, generally you will want to make four separate partitions; namely, / (root), SWAP, /tmp and /home.
You will want to give the root (/) partition around 80 GB for all of your software needs. Rule of thumb with the SWAP, double your RAM (however, if you have a lot of RAM, then one to two GBs will do). The /tmp you will want to give a good 15 GB or so, this is where data will be held temporarily, e.g., backing up a 4 GB DVD, the 4 GBs will be held in the /tmp and removed after the copy is complete. Thus it won't impact your main memory). And last, your /home partition. Give that the rest or give it 100 GBs and the rest as a separate backup partition.
When you need to reinstall, be sure to manually setup this same partition layout, and MAKE SURE that you do NOT format the /home (and don't even worry about touching the backup partition if you have one).
To further elaborate, you will click on the root (/) partition, set the proper Filesystem (e.g., ext4), and select to format. Do the same with the /tmp, however, with the /home partition, set it as /home, and DO NOT format it. Don't touch the backup partition if you have one. (This will keep all of your personal data in tacked while reinstalling or upgrading the OS!)
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If you have another HDD and have formated it to ext3 or ext4, it will be set as owned by root. You need to manually change ownership. E.g., if you have a backup partition labeled "backup001," the you need to open a terminal and input:
sudo chown -R username:usergroup /point/of/location.
(Let User Name be mark, and mounted location in media)
sudo chown -R mark:mark /media/backup001
sudo (uses admin privileges)
chown (change ownership)
-R (reclusively; that is everything in that partition)
mark:mark (setting owner to user mark and group mark)
/media/backup001 (Partition)