Plotting points simply means measuring the points on the groundplan so you can tape them out on the rehearsal room floor.
You want to make sure you plot out the edge of the stage, the proscenium, everything permanent to the facility, and then start plotting the points for the set. Every wall, every window, every step, every escape step, masking used for the production, everything you see on the groundplan that an actor could touch, run into, step on, look through, etc should be taped onto the floor.
I use downstage center as my zero point, and start plotting (measuring points) downstage left, working my way around the set counterclockwise, labeling each point on the groundplan with a letter, and marking it's coordinates on a separate piece of paper. When it's time to tape out, I use dots labeled with corresponding letters to set the points on the floor and then taping out becomes a big game of connect the dots. It may seem like an extra step, but it actually makes taping go a lot faster if you put a little more effort into plotting.
Some undergrad programs swear by a method of taping out that uses triangulation, which I find to be an utter waste of time as it is not precise (for me).
Hope this helps . . . .and don't be afraid of messing up. Worst case scenario is you have to re-measure a point, or use your best judgment to come up with a point that is close enough.