Do you have your PSoC HID connecting and enumerating with the host PC as a HID? If so you just need a way to talk to it from the host PC in your language of choice.
I built a quick application to display data from a PSoC5LP based HID device in WinForms C#, I used HIDSharp to interface with it. I haven't worked a ton with it, but it worked for me to send some bytes back and forth. There are other options for other languages. PyUSB For Python for example. AN82072 can help here.
As far as getting the PSoC configured and using the USBFS API in PSoC Creator goes, it's more than just setting up the USB clock. You need to configure the USBFS component and tell the PSoC how to arrange the incoming/outgoing USB bytes. HID has a set of rules for how it needs to work, AN57473 was a huge help getting me started, and comes with some very helpful examples.