I feel you, bud. I had to make the fireballs in my Mario fangame fly straight instead of bouncing along the ground.
Additionally, I'm not sure how to achieve the replacement of individual ordinary tiles in GBS. When I try to replace one, all identical tiles get replaced together. This forces me to resort to character sprites. However, the Game Boy's hardware should be capable of achieving such an effect. For example, in "Harvest Moon," using a hoe to till the land replaces each tile individually as it is tilled.