If I understand your problem correctly, you are trying to download very large files (probably overnight or something?) but your computer ends up going to sleep after X minutes of inactivity and interrupting the download?
If that's the case, the easiest way to solve it would be to change the power management options so that the PC won't go to sleep. If you have windows 7, the power management options can be found on Control Panel>System and Security>Power Options. Just remember to change it back when you are done with your downloads or you'll waste electricity.