All straight fertilizer, basic and quality, will only apply on bare tilled earth. You will need to put it on the ground before you put down the seeds. If you try it afterwards with the seeds on the ground it won't even attempt to use it.
As DanmakuGrazer points out in the other answer, alternate soil buffs like speed-gro and water-retaining will still work at any point (tilled, planted, or even halfway to harvest), so long as there's not any other buff in the soil already. I am not certain if you would get a full benefit from speed-gro planted mid-cycle, but that seems doubtful.