How big is your hdd's ? I use my 320gb for windows 7 ult 32bit and keep every type of file organized in diffrerent folders.
To prevent any problems I split that hdd's space into 2 partition about 160.00 each.
Download defraggler and tell it in the configuration to only defrag when your not on your pc and move big files that are being used the most to another part of the hdd platter.
Take my advice and tell defraggler to work between 2am-6am.
Use CCleaner to keep the windows resources and managment cleaned up and up to date.
Microsoft security essentials or even avast have them start up after defraggler is done working.
I know some people hate utitlity suites but give system mechanic 10 standard a try.
It does it's jo correctly and won't disturb you until you leave the computer alone for more than a hour.
I don't know if you fold or not, but if you do, give your cpu a chance to cool down from working very hard.
As a matter of fact get into the habit of shutting your pc off on saturday morning or saturday night.
Last keep your computer parts clean, it will be a little bit better if you wipe up everything after 2 weeks or so.