Jot uses three customizable mini-templates. One for the form, one for the output (this gets applied to each comment) and one for the moderation. You can adjust your tpls in any way you please.
The default tpl can be found in assets/snippets/jot/templates.
The best way to do this is to copy the default form (chunk.form.inc.html) into a chunk, specify your chunk in the &tplForm=`chunk-name` parameter of your Jot snippet call, and make sure it works as expected. Then make the changes you want to the form, checking to make sure it still works after each change.
These tpls appear overwhelming at first, since they use PHx modifiers heavily, but they are very flexible once you get used to it.
There is no need to install the PHx plugin since Jot has its own phx class file that it uses. Jot's and Ditto's phx works exactly the same as the plugin, so the documentation here will be useful.
http://wiki.modxcms.com/index.php/Jot
http://wiki.modxcms.com/index.php/PHx
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*happy dance*