Just add the domain. Google will figure out the rest.

My site is huge and has four sub folders that is why i am a little concerned here

Add and verify the domain; that's all that's required. There's no need to be worried about anything.

Don't get confused. Just the domain name will work. Whether the website is big or small that doesn't matter.

Just add your domain in Google Webmaster Tool when your site is live. Google will find rest pages or sub-domains.
Don't forget to add www and non-www version of your website and then set a preferred domain to get more traffic from search engines.

All right. Thanks. feeling rather ok now

Adding the domain alone is the good practice , no need to go for sub directories.

Google is a huge company. There algorithm will take care of everything.




Cheers,
Mark

I agree with previous messages, but if you have different sites on those folders, you will need to install the code on all those subdirectories.
For example, you could have installed a joomla website on www.mysite.com and a wordpress site on www.mysite.com/blog. Those are 2 completely different sites that will need different Google Webmaster Tools installations.