> Sharpie will come off when you clean the board of flux unless you are very careful and protect the area. Or you have to leave your board covered in flux splatter from the soldering.
For boards I intend to clean, I use Kester organic core lead solder. Rather than the usual rosin, the flux core is some organic acid, which is water soluble. Usually it only requires running water over the board, toothbrushing at most.
Don't use it on anything you don't plan on washing, though. It'll corrode traces over time and the residue is apparently capacitive. It'll make CMOS logic and OP-AMPs oscillate.