So what u really mean was that I can always run jkdefrag even without checking errors on my drives?
JkDefrag accesses harddisks through Windows, just like any other application. It simply instructs Windows to move a file to another place on the disk. It does not access the disk by itself and does not mess about in the MFT. It therefore cannot get confused and cannot scramble things if there is something wrong with the disk. It's windows that is doing things, not JkDefrag.
You don't check your drives for errors when you want to run Word, or Outlook, or any other application that read/writes to harddisk, right? You might argue it's a sensible precaution, and I will have to agree on purely theoretical grounds. But there is no need. Like I said before, Windows if pretty good in detecting errors on the harddisk and protecting your data. So my answer is yes, you can always run JkDefrag, without first checking your disks for errors.
By the way, it's still a good idea to backup before defragmenting, just like with other defragmenters, because the heavy use of the harddisk may trigger a hardware fault.