I dont know, i dont know much about Ipods and wether they can be configured to 2 seperate drives
What it looks like you might have to do is buy an external HDD, transfer all your music/films onto it (assuming the new HDD is bigger than the one thats in your PC) once thats done i think you might have to re-format your Ipod from scratch and transfer the data over from the new HDD.
But dont hold me to that, im not to clued up on Ipods
I dont think it matters which drive it is on with a ipod because Itunes controls all of the music or films. As long as when you have your ipod connected you have your extrenal HD connected you will be fine!