This page may help you to exclude  folders from your backup. Excluding folders from your backup is easy with WPBackItUp. There is an option to filter your large files that leads backup to fail. In this way your backup folders with too large files will be put out as you run a backup. 


To exclude folders go to WPBackItUp Settings and scroll down to the “Filter your files” section.  It is important to note that when a folder name is present in this list any occurrence of that folder, and all its contents, will be excluded from the backup. You can exclude any folders in the filter section. 


http://support.wpbackitup.com/solution/articles/5000676649-backup-problem-filter-your-folders