Practice! LOL!

Here's how I do it: grab the pants with both hands at each end of the crease and place as flatly on board as you can. THEN, using the palms of your hands, run over the pants starting from the center, to smooth out any wrinkles that may be present, making sure not to "roll" the crease away from the edge. Keeping the pant leg tight using your free hand, carefully iron the crease FIRST, starting at the middle and working your way to both ends.

Hope that helps. and practice, practice, practice.

It's best if you follow the old crease lines. Lining up the outer and inseams works from hem on up to around the knee, and then it goes wonky due to extra fabric needed in the inseams area for sitting & walking.
Keep the crease on the straight grain and follow those old crease lines. Sometimes dampening or misting with a white vinegar & water mixture will help set the crease, but it depends a lot on the fabric. Worth a try, though, and it won't hurt the pants.