You can do both, and in between there is a third way of specifying different variables in variables.less to get e.g. a different font, or link color without much hacking involved. It really depends on how much you intend to deviate from the standard look.

Over time, as more people re-use Bootstrap, it seems to be getting more customisable with less hardcoded assumptions so more is possible just via variables.

Bootswatch has some examples of how to make things look quite different while not diverging too much from Bootstrap code so that you can pull in upstream changes with relative ease.

LESS is pretty cool, even aside from Bootstrap, so it might be worth looking at that anyway.