The command line option
--batchmode means that SpiderOak will do all available work (scan the filesystem, then build and upload everything in the queue, download and replay transactions from other devices), and then exit. This is a good option for scheduled use. You can add this to a cron job, or just run it yourself periodically whenever you want to update your backup set.
SpiderOak is also careful not to start more than one instance of itself at a time. For example, if you schedule SpiderOak to run in --batchmode each night, and for the first few days, SpiderOak has so much to upload that it does not finish before the next scheduled startup time, you don’t need to worry about coming back to find several instances running.
Before running --batchmode, you'll want to run SpiderOak with the --build command to scan for and build all possible transactions, and then --batchmode to upload all work generated by the build command. (Don't worry; --build exits without creating further changes, so you won't have runaway processes.)