1) By default, the program will use all of the available CPU cycles you are not using. In the unlikely event that this causes your CPU to run hot and interferes with your normal operation you can "throttle back" the program. This is an option when you configure, you can set it to use some number of cycles below 100%. (It folds proteins slower.) You can change the configuration any time you want. If you need help doing it, just let us know.
2) While folding, the program saves it's work to your hard drive periodically, so that if you shut down or lose power it doesn't have to start over from the beginning. The "saved work" file on my PC is taking up 407Kb. (Much less then any of my Ann Coulter pics.)