The program is self explanatory - read what it says in Step 1 and after doing that, click on Step 2 and open the Pre-Scan then wait for it to finish.
If that finds anything to repair then use the relevant buttons.
If it finds corrupt Package files then post the log where Julian or Shane will upload them for you to copy into the respective folder, then click on each Step in progression, clicking the relevant buttons.
When it comes to the chkdsk, use the lower button for it to run on the next reboot as a chkdsk in read-only mode can give false errors and you would have to run the other one then anyway.