If you run it in a virtual machine (personally, I much prefer VirtualBox to VMWare) making a flash drive is not necessary. Simply mount the ISO (you can even make a VM with no hard drive defined) in the virtual CD-ROM drive and boot.
You will lose some features (i.e.: you need a USB dongle for Wireless / Bluetooth hacking, no CUDA) but that will give you really quick access to all the tools.
You can also install BT to a hard disk in a virtual machine, which will allow you to save changes (install new tools, updates, register nessus, etc.) You don't need to worry about partitioning then, as long as you have enough free space it will simply create the partitions in a file on your host.
And then there's the dual-boot option which will give BT more RAM and direct access to your hardware.