Depends on what file you have. Now that you have S-on, you need to use either an appropriate PC36IMG RUU or an RUU.exe that runs from your PC.
This file is the latest RUU you flash from Hboot, rename to exactly PC36IMG place on the root of your SD card:
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Power down, Hold volume down and power simultaneously until hboot appears, hboot should scan and find the file, select update, phone will do it's thing, be patient it taks a minute. Once phone reboots you should be good to go.
Let us know how it goes.