Connect PICKit2 to PIC18F14K50
In your case you can leave pin 6 of the PICkit unconnected. You wont need it. Pin 6 is, as far as I can remember, for devices that need a special codeword to get into programming mode.

You dont need to seperate the programming circuit from your rest of the circuit, when you follow some rules (See Section 3 of the PICkit 2 manual):


You should take care, that the "VPP voltage slew rate is not slowed down". So dont put big capacitors on the reset pin or you will get in trouble.
The signals of the PGD and PGC pins shouldn't be affected. The manual of the PICkit suggest the use of some resistors to isolate your signal (see the figure below, taken from the manual). But this depends heavily on your external circuit.