I was running defrag and had to stop it. After I began again, it went to this message:
"Disk defragmenter has detected that chkdsk is scheduled to run on the volume: (C)
Please run chkdsk/f." Since it won't go back into regular defrag, what do I have to do
To run chkdsk?

You have to restart your computer and then it would run at reboot.

You can run Defraggler (http://www.defraggler.com)