You will need to download the initial bootstrap file (upload fewer files), add fewer files to this source and then compile to get bootstrap.css, which includes your changes.
The steps for downloading the source file and compiling it are here: http://getbootstrap.com/getting-started/
Before compiling, add your custom less file import to bootstrap.less
@import "myvariables.less";
Be sure to add this import as the last import so that your changes are not overridden.
Compile your bootstrap source to get bootstrap.css, which should have your changes.
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