Hard Drive Assistance-Closing Files

Hi, Windows XP Pro, AMD 1500, 2 Hard drives, 30 and 120 Gigs. Both Seagate. I ran the online Seagate diagnostic and it tells me that I have errors and should run chkdsk /f (on both drives). I defragged both drives (they were pretty fragmented) and ran the diagnostic again. Same result. I ran Chkdsk and it told me it couldnt launch because I had open files, but on restart would run the chk. I restarted, it went thru the process. Ran the chk, same think open files. Question. How do I close the files to get a good chkdsk. Question two, how do I launch chkdsk for the second drive? Second drive is used for storage only (music, photos, video, etc). I have an onboard HDD utility 9HDD Health) and its reading both my drives at about 52 C (I know its hot, how do I cool) My screen saver freezes shortly after it comes on. Are the HDD problems causing this. All help appreciated and like always thanks.
L