Try GParted. It will allow you to make changes to anything you want. Be very careful!
You need to prepare all of the partitions before you install your OSs. Write down what your partition's names are and where they are (including the ones on your hard drive) so you don't destroy anything you don't intend to.
Or you can use UNetbootin if you are looking for an easy way to get installation media on the flash drive.
Make sure you back up anything important before you do any of this of course.
If you want to have Windows on the system too, make sure that you install Windows first as it will usually delete anything else it finds otherwise.
If you Have Windows installed already and have Ubuntu on a disk, when you go to install Ubuntu with your disk you should be given the option of doing a dual boot. Ubuntu Windows Dual Boot
Hope that Helps.