You can use PICKIT3 programmer, you just need to add it correctly as a tool in your mikroC PRO.
When creating new tool, give it a name, browse for and put PICKIT3 programmer file path in File Name menu.
Then you have to set up Parameters for that tool. In order to set up parameters, you should firstly see what command line format does PICKIT3 programmer expect and use that format for parameters.
I don't have a PICKIT 3, I have a clone pickit 2
and those steps work well.