I actually do a combination of both... I make a copy of my pattern and use a metal board with magnets (or I tape it to the board) and then I use a marker or pen to mark through each line of the pattern.. I can't keep track otherwise.

Also, if it's a pattern that has a repeat, I'll make two copies and then cut and paste the repeat into the appropriate place so I can mark through each line.

There's something satisfying about looking at a pattern that's mostly black lined and KNOW you're almost done! Progress is my friend!