What's the recommended way to override core bootstrap styles?

I'd like to make some changes to the bootstrap default style. For instance, change the padding for the navigation elements.

I noticed that when I change the LESS code for bootstrap (in /plugins/system/t3/base-bs3/bootstrap/less/variables.less for instance) the changes do not get recompiled when I use the "LESS to CSS" button.

What is the recommended method to make these changes? And how can I recompile the LESS for the bootstrap core?