Hello, Yvan.

When you click the "Syncing" button in the toolbar, and it turns green, Smarky installs what Apple calls a "launchd agent" into your system.  This "agent" watches your Safari bookmarks.  When a change occurs, the agent launches a process which sorts your bookmarks.

Although this agent will also work when Smarky is running, it can be annoying and uses more system resources.  You should not make Smarky a Login Item.  You should launch Smarky whenever you want to do major bookmarks housekeeping or reorganization, then quit it when you are done.

If you want more technical information, read this section in the Help Book; sec. 4.9.4 in particular.

Tell us if this does not resolve the issue.