I use black "Sharpie" brand permanent markers for marking the PCB. For some reason, these seem to be the best for PCB work. I don't know of any other markers that will work. Also, after marking, you may want to let the ink dry for a couple of hours. Even though the ink feels dry, it still needs time to fully cure, or "harden" so to speak.
What I would do with your almost etched board is to rinse it off in water for a little bit, then use solvent to clean everything off including the markings, and start over. Make sure that the PCB is extremely clean or the marker wont properly adhere to the copper surface, which could lead to poor leads and pads. See if you can salvage the board this way. If not, I would suggest starting over. Make sure that you go back over your markings over and over again, to make sure that the ink is on pretty thick. Dabbing the ink onto the already drawn lines works pretty good because it wont create streak marks.
Also, did you warm the Ferric Chloride up before placing the PCB in to etch? You don't need to boil the Ferric Chloride, but a warm mixture works a lot quicker than room temperature Ferric Chloride. As you may have learned, the ink isn't going to last forever in the bath of Ferric Chloride, so having a quick working solution (Warmed up) is to your advantage.
Finally, by agitating (Rocking, or carefully swishing) the container while the PCB is in being etched works well too. This removes the already etched copper "layers" as the Ferric Chloride works to etch the board.
As with anything, the first try isn't going to really turn out the best, but with continual trials, and getting used to the process, you'll begin to learn the tricks. Don't give up, making nice boards using this process is possible.