If the other partition was created with BootCamp it can be deleted in Bootcamp and merged back into OS X.
It might be possible to rename the partition "BOOTCAMP" in Disk Utility and formatted MSDOS to trick Boot Camp into thinking it is a Bootcamp parititon and merging it back into OS X. (haven't tried this so I don't know if it works or not yet) I would first make a clone below before attempting this method.
TimeMachine restores are fraught with problems on these forums.
What I would do in your case is use another equal or larger sized (than your primary boot drive), blank, Disk Utility HFS+Journaled formatted, external powered drive to Carbon Copy Clone your OS X boot partition to it, then Disk Utility > Repair Permissions on both (you can ignore the list that shows).
What this does is gives you a "hold the option key" bootable clone, which while booted from it, check it out first and then use Disk Utility to completey (select the hard drive name) format the entire primary boot drive (HFS+ Journaled of course).
Then simply CCC back onto the primary boot drive. Then run ALL of OnyX's maintainence and cleaning aspects and reboot. Speedy machine here we come. (note: Cloning optimizes the drive by the order of the alphabetical order files in the Root Level, leaving "Users" last where the most change and slowdown in drive performance occurs, OnyX cleans out the caches and rebuilds Spotlight, more performance)
The new version of CCC has gotten a bit more complicated, including a archiving of files changed from between updated clones, however the default settings are fine for your first time clone to a blank drive. So all you really have to do is select the "From" and "To" drives and click Clone.
Clones are wonderful, it's a exact copy of whats on your primary boot drive, so far in the many years I've used clones everything has worked on the same machine, everything.
TimeMachine drives are not bootable, leaving you stuck if your hard drive dies or you can't boot from the OS X install disks.
You can first make a clone so you have that method, then c boot off the 10.6 installer disk and use TimeMachine that way to restore to the newly formatted drive (use Disk Utility under the Utilities menu, second screen in) I haven't tried this myself, prefering clones instead as it's less headaches.
Remmeber to ALWAYS have two backups of your data at all times, (erasing your drive leaves you with only one copy) in this case you would have a clone and a TM backup, in case one method fails (less likely the clone), then you got the other method.
There has been a few reports of issues with drives of that size as OS X or Disk Utility was unable to address it's huge capacity.
When you format it, chose the Security Option Zero all Data, this will take overnight, but test the drive to make sure it's completely accessible as well as map off any potential bad sectors.
Data retained on the drive will be more reliable as well.
CCC worked wonderful for me. I copied the data (ripped DVDs) from the other internal 500GB drive to the 3TB drive. Then I cloned the partitioned drive over to the freed 500GB internal. Selected that as my startup drive. Tested it for awhile and worked well, combined the two partitions on the other internal drive and formatted. Now things are great for me.
Yeah, I think a bootable drive is even better. If things go wrong, just copy it all over and start over. Or you can just run from the bootable drive until your other drive is fixed. I am apt to use it more so than time machine.