I'm just documenting this, hopefully it will be helpful to new users.
The original discussion for this arose at
fStew provided a simple answer which the following is based on (some updates due to rename of the project).
Benefits of a subtheme
If you use a subtheme, you can make changes to your own template files separately and easily keep the bootstrap theme up to date.
Creating a subtheme
1. Create a new theme folder with the name of your theme. e.g. subtheme
2. Add an .info file (see example below) - e.g subtheme.info
3. Create a .css file for your subtheme css. - e.g. subtheme_style.css
Note that the bootstrap theme itself doesn't need to be enabled for the subtheme to work.
name = subtheme
description = Bootstrap subtheme
version = 0.1
core = 7.x
base theme = bootstrap
regions[navigation] = 'Navigation'
regions[header] = 'Top Bar'
regions[highlighted] = 'Highlighted'
regions[help] = 'Help'
regions[content] = 'Content'
regions[sidebar_first] = 'Primary'
regions[sidebar_second] = 'Secondary'
regions[footer] = 'Footer'
stylesheets[all] = subtheme_style.css
settings[toggle_name] = 0
settings[toggle_search] = 1
If you want to override templates provided by bootstrap, create a
templates folder and copy over the template you wish to override (e.g. page.tpl.php).
You can learn more by reading: Creating a sub-theme
If anyone has other suggestions to add to the subtheme, we can try add to the documentation.