I think you understand how to use the starter tool on the site, but its the actual building of the starter that is tripping you up.
So when you are going to a second step make sure that your yeast are done doing their thing, which can be anywhere from 24-48 hours depending on the viability of your yeast. When I step my starters up I simply add the require amount of wort on top of the existing starter, aerate and let it go. So if I did a 1 liter starter and need another step and one more liter will get me to my target pitch rate, I will simply add another liter of wort once the first step has finished (2 liters total in my vessel). This is completely dependent on the size of your starter vessel, I will normally not fill my starter vessel more than half way in order to prevent a blow-off. If I don't have enough room I will decant before going to the next step. Before decanting put the starter in the fridge for 24 hours to allow the yeast cake to pack down nice and tight.
An important thing to note is that when using the starter calculator only put the amount of wort you plan to add at a particular step in as the starter size. So if i did step one with 1 liter and was going to add another liter at step 2, the starter size for both steps would be 1 liter. So I would be using two 1 liter starters, and not a 1 liter and a 2 liter.
Also I have uploaded some pictures of my latest starter to show before and after. Its the same starter just 24 hours apart. This starter ended up being 4 steps, in order to grow a slant large enough for a 10 gallon lager.