In the diagram there is a line of lights all pull string type. To convert, you must find the fixture that receives the circuit power first before continuing the circuit onto the next light fixture, you break into that fixture as illustrated in the diagram, this as in the diagram creates 2 3way switches that controls several lights.
The white wire between the fixture and the switch, wrap a black piece of electrical tape on the ends of the wire to signify that this is a hot wire and not a neutral. If using the 3-way switch then do the same with the white wire on the cable going between switch 1 & 2.
If you only want one 2 way switch to control the light(s) then only switch 1 will be needed with a standard 2 way switch. The black & white wire on the cable in the diagram going between fixture 1 and switch 1 would connect to the 2 screws of switch 1.
If you want to use only 1 light fixture then ignore everything after fixture 1.
Either leave the pull strings on , so that they are only controlled by the switch(s) or replace the fixture.
Bare wires are always together and if a metallic electrical box then ground to box. Non-metallic boxes do not have a grounding screw, just bares together and put an insulated wire nut on them.
Should a fixture have a ground screw or green wire - ground it too. If the switch has a green grounding screw on it then ground it also.