First, there will be some problems of NTFS if you use it Linux:
NTFS doesn't support file permission mode very well, so you'll lose the executable bit, setuid bit, etc.
The ACL system in NTFS is not so comfortable with Linux, and YOU CAN'T DISABLE IT just like FAT32.
Currently, the performance of NTFS implementation in Linux is a bit of slow. For example, I found it build a Maven project in NTFS is 3 more times slower then ext4.
Personally, I run Windows OS in VirtualBox, and make the virtual disk as a raw NTFS image, (see http://goo.gl/1I6gJ), Since the NTFS image now is in the raw format, rather then .VDI, you can access the NTFS by mount it directly, without power on the VM instance.
By using VirtualBox instead of Dual boots, there are several advantages:
You don't have to convert your Linux partition to NTFS file system, in the VirtualBox, you can use Share Folder to access the host OS's file system. And it's very fast. Map to a drive letter if necessary.
You can work on both OS concurrently, without restart to switch one to another.
Your GRUB loader will never be overwritten by Windows. Windows always overwrite your boot record and never prompt you yes or no.
You will pay more attention to Linux, and then you'll find the Linux way to do most of your work. In fact, I found it's rarely needed to turn on the Windows VM day after day. Because people are lazy to learn new things, if you installed dual systems, and Windows is just enough, why will you bother to boot into another OS?
I found this is the best way to make both Linux and Windows coexist. And now I have built several Windows VM instances for different usages, because I don't install too many softwares in each single VM, they are running fast and I don't feel too much difference then the non-virtual ones.