I want to apply a custome look and feel for different subsites. My question is how to add css reference to specific subsites?
If the site has the Publishing Feature enabled, you can link to a custom CSS file in Settings > Master Page.
If the Publishing Feature is not enabled, you will need to edit the Master Page and inject your link to the custom CSS.
All this has been asked many, many times before and there are lots of web sites and tutorials explaining the finer details.