The usage is very simple: just type or paste your desired Chinese text into the home page's text box, and click the Add tone marks button.
There are several rules about tone changing in Mandarin that are used. You can find a description of these rules for multiple third tones, 一, and 不 on other web sites. www.hackingchinese.com has a very interesting web page on tone changes that covers the standard tone changes, in addition to others (which this website doesn't currently attempt). The three mandatory tone change rules are made automatically when enabled.
Outside of this web site, these rules are very rarely applied to changing the tone marks of written Hanyu Pinyin. The reasons for that are complex, but suffice it to say, it's not always the best idea to change them for printing, nor to not change them. There are good arguments both ways, but the standard has been not to change them. This web site gives you the option of changing them, and those options are on by default, because I think it's most often useful to change them for tonemarks on Chinese characters (as opposed to Hanyu Pinyin).
In the case of the multiple third tone rule, you may want to use your own variation of tones, depending on usage. The web site's implementation uses a simple algorithm to changes all continuous series of third tones to second tones followed by a single third tone. I plan to make an improvement that will allow you to manually and selectively change individual tones in the output to suit whatever need you might have.
Finally, there's an option for font size. This box will accept any legal CSS font size. The default is 4vw, which means each character uses 4% of the view window, which means the font size will change based on the size of the window. However, you can also use fixed sizes, such as "large", "16pt", etc.
When a character or word has multiple possible tonemarks, according to the dictionary, the output will show the different options within a set of orange parenthesis, separated by orange vertical bars. For example:
If you don't know which one to choose, you can consult an online dictionary (or other resource, such as the perapera Chinese extension for Chrome which is quite nice for this purpose). Once you have decided which tone option you want, just click on it, and the other options will disappear.
If you mistakenly clicked on the wrong one, just click the one you selected again, and the other choices will reappear.
This processing of text in this web site results in loss of formatting, such as newlines, tabs, spaces, etc..
When multiple tone possibilities exist for a word or phrase, the automated tone change system will not adjust tones relative to words outside of the selected word/phrase. This is because the automated tone changes are already complete at the time that the selections are presented. Fixing this problem would be very difficult, and won't occur very often anyway. When manual tone changes are implemented, that will lessen the impact this problem.