So here's an effort to show both at once. I'm using the Plot Browser as a legend and too turn things on and off (sometimes I'll make a whole group of lines one color or linestyle as well). You'll see that I have 7 figures docked here. That's not unusual for me. I often have more figures at one time (anything up to 15 is typical). I'll generate via a script and set them to specific figure numbers (not so much in this example - only the 101 and 102 fall into that category). The next step might might involved me reading results for a variation and I would plot those as 201 and 202. Let me lay out the scenario more specifically below the image.
1) Run a model in a finite element solver.
2) Run a postprocessing script in Matlab that reads the resuts, modify as needed, and plots into specific figure numbers, say 100-105. 100 might be pressure, 101 power, 102 impedance etc.
3) Dock those figures in the plottools window.
4) Run a variation of the model.
5) Run v2 (which is the same as v1, just with a different model name and results file as I usually write the scripts to take those two pieces of info at the beginning and everything else below is variable names) of the postprocessing and plot into 200-205.
6) Dock those figures.
7) Use the plottools interface to jump quickly between 100/200, 101/201, etc. to compare changes in the results. That let's you easily see how the frequency or magnitude or shape changed from one version to the next.
8) Use the Plot Browser as a legend since there might be 40+ lines on the plot and as a way to turn off currently undesired lines (and then turn them back on when I want to look at that part of the results) or change color/style.
9) Possibly update scripts to explicitly plot what I've been testing manually (in terms of color, style, which lines etc.) in the Plot Browser.
10) Run more models and repeat.