The WDC NanoLounge

You update it manually.

For your Writing.Com NanoCounter, Just click on your wordcount (which is "1" by default) and you can both update your wordcount throughout the month and put the item number for your Nano item.

For your NaNoWriMo.org counter, you can copy and paste your manuscript into their website, like Ember Rain said, but once November starts, you can generally just type in your word count throughout the month, instead. You are only required to copy and paste your manuscript into their website if you want to verify that you've got 50000 words (or more) and become an official winner.

-Mariah :)