Using bootstrap on Vanilla 2.1. What is the correct way to override the bg color thru the whole theme. Thanks.
Follow the install instructions, modify the appropriate style LESS file, and recompile the CSS.
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As @hgtonight says, the proper way is to edit the style's LESS file, which you will find in bootstrap/bower_components/bootswatch/theme_name_folder.
Take a look in the variables LESS file, and you should find the setting for background colour declared as @body-bg:
Once you have done that, follow the instructions to recompile.
If you don't want to go the LESS route, you can also add the appropriate css rule in the custom file you will find in bootstrap/design.
If you plan to make a lot of alterations, I would recommend getting the hang of how the LESS files work.
See here for a brief intro: http://www.hongkiat.com/blog/less-basic/