how to add custom left navigation bar using css at sharepoint 2013. Does this custom bar apply to all sharepoint pages?
Yes custom bar will apply to all the SharePoint pages, there is nice series of articles to customized it, here is the link of it, in this you will get link of previous parts also.
I assume you are using the CSS to just customize the branding of the left navigation. If so, you will be able to apply it for all application pages by simply adding the custom CSS to the current masterpage for those pages and making sure you are overriding the sharepoint left menu navigation control styles through your custom CSS.
Here are some good examples of doing just that: