Can't delete partitions/Partitions look like separate disks in Disk Utility

I don't even know how I got to this point, but I'm guessing I did something careless... As the picture above shows, Disk Utility appears to show my machine as having three disks. However, it actually only has 2. "A" and "B" are two partitions of one disk.

Before any of this, I had the same two disks (the one containing A and B and the 640-GB one outside the box) but a different setup among them. The disk that now shows in Disk Utility as two separate disks ("A" and "B") was my Macintosh HD running OS X Yosemite 10.10.4. The other disk (the 640 GB one shown outside the box), which is now "Macintosh HD," was the disk that contained Windows Boot Camp. The disk that I'm having trouble with (A and B) is 3TB, and I decided that it was a better location for my Boot Camp installation since I have a large amount of local file storage in Windows. Furthermore, the 640 GB HD is easily large enough to serve as my Macintosh HD because virtually everything I work with in OS X is stored among various cloud servers.

SO, I created a bootable install of OS X Yosemite. Before the installation, I used Disk Utility in recovery mode to partition the 640 GB HD for OS X installation. Next, I tried to erase the 3 TB HD (A and B). I could not select the erase process, but I could choose to partition it. Under the partition option, it already displayed the original Macintosh HD, which I could not erase and shrink down past a certain size. I'm guessing now that this is because the partition contained my original OS X Yosemite installation. In any case, I created a FAT32 1-TB partition and named it "Windows HD," which I intended to hold my new Boot Camp installation. I was fine with this because I don't need 3 TB even for Windows, so I figured I could have my Windows HD and then use the old Macintosh HD partition I couldn't get rid of (the remaining 2 TB) for backup storage.

The installation of OS X Yosemite went well. Once that was settled, I went into Disk Utility and attempted to erase the old Macintosh HD and format it as FAT32 to use as backup storage for Windows. It was during this process, that I got to where I am now. Before this "A" and "B" were displayed together under the complete disk (as partitions are usually displayed) and now, they are displayed as the picture shows (as if each partition were a disk itself), one containing "C" and the other "D."

Sorry, for the length of this post, but I wanted to be as thorough as possible the first time around. I'd appreciate any help!

Mac Pro (Early 2009)

OS X Yosemite (10.10.4)

2.66 GHz Quad-Core Intel Xeon

12 GB 1066 MHz DDR3 ECC

Startup Disk: Macintosh HD