They hit all the heads of the tricep - I am pretty sure all tricep exercises hit all heads, but the emphasis is placed on different heads with each exercise.
If you're doing the whole stack, you could try pinning extra plates to the front or resting a DB on top of the stack. I've pretty much stopped doing triceps pushdowns but I always liked to feel as much weight on them as I could manage. The gym staff weren't happy with me for overloading the machine but breezing away for 20 or 30 reps isn't my thing.
Alternatively, you might find you have more weight available on the lat pulldown machine even if you need to stand on the seat.
I wouldn't get yourself concerned with what head of the muscle is hit, because honestly, you're not going to get anywhere. You won't isolate one head of the tricep and completely ignore the others. Train the muscle with compound movements. Make steady progress. Eat a lot of food, enough to add weight to the frame.
You'll end up with bigger triceps. The shape will be determined through genetics, not training.