I took apart a 3tb Seagate GoFlex Desk external hard drive to put into my computer, but disk managment says that there is one GPT Protective Partition and two sections of unallocated space. The thing is I have files on this drive, so I can't get access to it without formatting it completely. Any help?
What exactly is your question here?
To do any risky operation on a disk you should backup all the important data anyway, so do that, copy all the files to a different disk/cloud whatever you can and then put it into your PC and partition it.
If the partitions show up as unallocated even on the external hardware then you are looking at data recovery, you can use testdisk or recuva for simple free recovery tools (always save to a different disk and not the one you are recovering from)
The enclosure is configured with a sector size of 4KB. When you install the drive inside your computer, you expose its native 512-byte sector size and render your data inaccessible. Sector 0 is still in the same place, so you can see the partitions, but every other sector is displaced by a factor of 8.
Reinstall the drive in its enclosure, backup your data, then copy it back again when the drive is inside your computer.