Installing new internal hard drive.  How do I safely clone my existing BOOTCAMP partition?

I have a 13 inch Aluminum Late 2008 MacBook.  Processor 2 GHz Intel Core 2 Duo, Memory 4 GB 1067 MHz DDR3, Software Mac OS X Lion 10.7.4 (11E53).  Currently I have a 160 GB SATA disk as my hard drive a d 4 GB of memory.  (Is it time to upgrade or what?)  I recently bought a Western Digital 1 TB internal hard drive to replace my exisiting internal hard drive.  I spent a lot of time last night trying to first- connect this new hard drive to my computer so that I can then clone the existing hard drive and then hoping that I would get that done so I could install the new hard drive.  No such luck.
My current hard drive is partitioned as follows:
Name:  Macintosh HD
Format: Mac OS Extended (journaled)
Size: 132.5 GB
Name:  BOOTCAMP
Format: Windows NT File System (NTFS)
Size: 26.69 GB
When I was partitioning the new drive I did so as follows:
Name: Macintosh HD
Format: Mac OS Extended (Journaled)
Size: 973.51 GB
Name:  BOOTCAMP
Format: MS-DOS (FAT) ---  This was the only option that I was given that I thought would work.  I did not have the option of "Windows NT File System (NTFS) to choose from.  Question # 1: is that going to be a problem?  I only run 1 program on Windows and that is the only reason I have BOOTCAMP on there at all.  However, I do HAVE to have that program.  Like I said it didn't give me the option to choose Windows so I didn't know where to go with this.  Any help with that would be awesome.
Size: 26.34 GB  (I just used the same size that was current, or close to it.)
I connected the Western Digital 1 TB through an external device, partitioned it as stated above, and then used Carbon Copy Cloner to clone the drives.  The first one went through fine.  (It took 2 hours and I went to bed before it finished.)  This morning I woke to see that it had gone through well.  I then started the process with the BOOTCAMP drives.  However, before I started it gave me errors stating that I wouldn't be able to run Windows off of the Cloned BOOTCAMP drive.  Question #2:  Is it because of the Format type I chose when partitioning?  Or something else?  I am unsure where to go from here.  I would really appreciate any help that is out there.  I would love to get this new drive installed ASAP.  Thank you so much in advance!

Well yes and no.  I succeeded with the clone.  All of the information seems to be there.  However, it isn't showing in the system preferences - start up disk -- as a start up disk option.  Therefore I assume it didn't clone correctly, or at least not in a way to use it the way I was.  I am thinking it may be a better idea to just run Parallels or a similar software program.  I rarely use the software that has to run in Windows.  And maybe that will be the easiest way.  I think I will still have to change the way I have it because I assume if it isn't running as it was before now I must have done something wrong.
I am unsure of where to go from here.  But know that I really do appreciate your help. 

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