I think practice is definitely a part of getting proficient at it. Using the 'align to grid' feature with the 3x3 squares just helps to get the map to the correct size, but it won't help with actually placing the map in the correct location. This is especially apparent when the map has a border that is a different size than the grid, because it won't align properly all on its own. After getting the map to the right size (or really close using the 'align to grid', I've found it is easiest to start at the top left corner and align the top-left-most grid as best I can, then go all the way to the right side of the map and manually adjust the width of the map image so that the right-most grids are aligned. you might have to do that a couple times as the left-most grid will be slightly resized as well. Then repeat top to bottom. Keep in mind that the Roll20 software has no way of recognizing where horizontal or vertical lines are on a map image. So there's no AI or anything that can automatically align map lines to the Roll20 grid lines without the GM doing it manually.