Hi Kat,
It should be all fine, whichever way you do it?
Which backup plugin crashed your whole site? Normally a backup plugin has no hooks into a site's front-end; if running a backup makes your whole site disappear, then usually the real problem is that the web hosting company has far-too-low resource limits, and shuts off your site if you try to run a backup - the only real solution to that is a better web hosting company.
David