In order to backup any file, SpiderOak must make an encrypted copy of that file and temporarily save another copy of that file. For example, let's say you have a 10GB file that you have selected for backup. There will be a temporary copy of that file in SpiderOak's data directory (actually, inside of a database.) This file is actually the encrypted blocks being uploaded, and the copy is retained until the server notifies the program that the transaction has completed. After that, the temporary file will be removed.
If you don't have enough space on your system, you can move your SpiderOak data directory to another location, and start the program, using either the --datadir runtime parameter or SPIDEROAKDATADIR environment variable to specify the alternate location.