If you haven't got bent pivots or cracked/chipped jewel then the balance wheel is bent, not good for isochronism. I personally true balance in calipers and would suggest this is the best place to do it.
There are two Truing processes, one in the flat and one in the round , always start in the flat first. Start at the balance arms always flat these first and then when the balance is true at the arms work your way round until the balance is flat. Small amounts of pressure can alter the flat quite easily, so no hammers involved!.
Truing calipers are made for this purpose, the balance staff does not sit on the smallest pinion but sits on the first shoulder of the pinion. On good quality Truing calipers a hole is seen a short distance from the end of the bush, with a good loupe you can actually see into the hole and see if the pinion ends are straight themselves when the balance is turned in the calipers, just make sure the calipers are fairly tight up to the staff shoulders before attempting truing, you don't want to break the pinion so.
There is an adjustable Truing gauge attached to all good Truing calipers, it's there for a purpose. You will notice a small vee in the Truing gauge, this allows you to miss any adjustment screws that may be in the way of the gauge when rotating the balance.,
Truing in the round is a different matter but still done in the Truing calipers. Best tool for this is a small flat notched lever bar. This sits over the rim of the wheel and is used to bend the rim inwards or outwards. It's specifically thin to get into the gaps between the adjustment screws. Always true from the top of the balance wheel, not the bottom.
It takes time and can be frustrating, but with practice it's doable. Don't forget to check poise afterwards!.