i'm by no means an expert and I have not tried the pickit3 (I have and love my pickit2)
I also have PBP3

you should be able to set your configuration bits by doing something like the following...

Code:
    #IF __PROCESSOR__ = "16F1828"
        #CONFIG
        __CONFIG _CONFIG1, _FOSC_INTOSC & _WDTE_ON & _PWRTE_OFF & _MCLRE_OFF & _CP_OFF & _CPD_OFF & _BOREN_OFF & _CLKOUTEN_OFF & _IESO_OFF & _FCMEN_OFF
        __CONFIG _CONFIG2, _WRT_OFF & _PLLEN_OFF & _STVREN_OFF & _BORV_25 & _LVP_OFF
        #endconfig
    #ELSE
        #IF __PROCESSOR__ = "16F690"
            #CONFIG
            __CONFIG _INTRC_OSC_NOCLKOUT & _WDT_ON & _PWRTE_OFF & _MCLRE_OFF & _CP_OFF & _CPD_OFF & _BOD_OFF & _IESO_OFF & _FCMEN_OFF
            #endconfig
        #ELSE
            #ERROR "Program does not support " + __PROCESSOR__
        #ENDIF
    #ENDIF

    #msg "compiling for target " + __PROCESSOR__
The above allows you to set the configuration bits for more than one processor.

NOTE: some of the configs above begin with just 1 underscore "_" and some have two
and I believe it is important to get that correct.