SaneBox only labels emails it finds in your Inbox. Also, we only manipulate SaneBox labels.
Your current labels will be unaffected except for the Inbox label. In our default mode, we remove the Inbox label when we move an unimportant item to your @SaneLater folder.
We have an advanced mode for Gmail called Messy Mode where all email remains in your Inbox, and when we label one as @SaneLater, we do not remove the Inbox label. This may be the best option if you wish to keep your current labels.
Note: Messy Mode has been deprecated. For grandfathered users of this feature who are seeking assistance, please open a ticket with support.