By default, Graphmatica labels the hatch marks across the graph with the number of their coordinate so that you can more easily locate points or find the coordinates of a graphed point. In some cases, though, especially when doing graphs near the axes, the numbers can be confusing and you may want to turn them off. To do this, select Graph Paper in the Options menu. In the Legends tab, select the No legends radio button.
Depending on your grid, window size, and screen resolution, you may find you need to tweak Graphmatica's Automatic spacing to get the best results. There are two sliders available to do this, one for legends and another for gridlines. Moving a slider to the left makes the spacing coarser (farther apart) and to the right finer (closer together). Note that since you are controlling the minimum spacing, and because in automatic mode the legends are constrained to be 1, 2, or 5 times a power of 10, and the gridlines are constrained to be whole units in between the legends, you may not always see a difference between two settings for a slider depending on the current grid range and window size.
If you find that, even after tweaking, the interval that is automatically chosen for the grid spacing is not well-suited to your task, you can set Custom spacing increments for legends independently for the X and Y axes by filling in the one or both of the edit boxes. (When you have selected Trig graph paper, you will probably want to use the constant "p" in the custom spacing you enter for the x axis so it is a multiple of π.) You may also enter custom grid spacing for both axes. If you leave any of these fields blank, automatic spacing will be used for that value.
If you select custom spacing, you can choose between two behaviors when the grid size changes: 1) Lock the legend spacing to the values you selected, or 2) Scale the grid spacing along with the grid itself. Unfortunately, neither option will be likely to satisfy you if you change the grid spacing by a non-integer factor or by too much, so you may have to reset the spacing to more suitable increments again manually.
You can also choose between positioning the vertical-axis legends above the gridlines (the default) or centered with respect to the labeled gridline.
Shortcut: You can modify the legends easily by right-clicking along the x and y axes (to get a popup menu with Edit Legends… on it) or double-clicking in the same location.