Yeah if you meet your opponent in the air with jumping fierce or double fierce, you need to walk up a little bit on the ground to line yourself up for the correct stomp distance.
As Blu mentioned, dashing is also an option sometimes.
There’s no trick or gimmick to the imput like with Cammy’s instant spikes, it’s just a clutch motion from up forward on the stick to straight down + mk.
Practice makes perfect.
I landed some clutch stomps the other day in a Chun mirror lol.
And instant stomp is always a great gimmick too