The corpse cart is always built with the "guy with the whip" driving it (or with the alternative sword arm, neither has any game effect). It would be up to your brother if it counted as just a corpse cart or a corpse cart ridden by a necromancer.
As for using the loadstone or balefire, I'd magnetize them if you're skilled enough, as both options can be useful in the game. However, most opponents will not mind if the model has balefire but you play it as having the loadstone in game (or vice versa) as long as you are clear about it at the start.
As for in game advice: mounting a necromancer on a corpse cart generally isn't very useful. The necromancer becomes exposed and you're adding two units together which have poor combat potential to create a unit that still has poor combat potential.
The balefire (is that +1 wound with invocation? I get the two mixed up) can be good if you keep it near the centre of your line and you plan to cast invocation of nehek a lot (not a tactic that I find works, but it has its advocates).
The loadstone (-1 to enemy casting attempts within 24") is also useful in the correct situations. It can level the playing field if you only plan to take a level 3 wizard for example. I find that with so many PD being thrown around in 8th it doesn't help much.
I've actually tended to field the corpse cart without either upgrade when I've used it in 8th edition, as I've only been using it for its bound spell.