Right now there's no way to do this automatically. We agree that this is important, and we'll be improving this in the 2.1 series of SpiderOak.
Right now you do have some other options though: You may run SpiderOak via it's command line interface. There are command line options for changing your backup selection, and running in "headless" mode (no GUI at all) or running in headless batch mode, where SpiderOak will startup, do all available work, and then exit when everything is complete.
You can see all the available command line options by running SpiderOak with