I am working on a Rails project that is just starting. We want to use twitter bootstrap as a base for our styles, at the beginning we would simply use bootstrap\'s class names d
I recommend you have a look at sass placeholder classes http://sass-lang.com/documentation/file.SASS_REFERENCE.html#placeholders in order not to bloath your css. Most likely you won't be using every single element included in bootstrap and placeholders only get written to your stylesheet if they are actually extended in your code.
Also, I think people tend to get confused about how css frameworks work and how decoupling css and html actually works. For very large websites (or ones that you expect eventually to grow very large), where performance and css file size is crucial, some kind of OOCSS approach is your best bet. And this means inevitably that you have formatting code directly in your HTML.
If you can allow yourself to be a little less efficient and want your HTML clean, make sure to use semantic classes (examples for buttons: call-to-action, call-to-action-secondary, submit, btn-primary, btn-corporate-color, etc...)
Also remember to decouple your JS from CSS! use special classes for attaching behaviour (example js-submit, js-call-to-action, etc....)
Last but not least: don't plan for updating your css framework. These frameworks are meant to give you a headstart, not to be your overall design solution. Extend them, adapt them, make them your own, invest in design and create your own look in order to make your app unique. If what makes you think of updating is a worry to keep up with standard changes, better use compass mixins.