To merge two different changes of one file back to the original file, use the 3-Way Merge. You can start it either from the Welcome dialog or by passing the base file and the two different changed files (left and right) as command line parameters.
If SmartSynchronize detects, that it can merge conflicting changes automatically, it will ask you immediately after opening the 3-Way Merge. To auto-merge later, use the menu item File|Auto-Merge Changes.
With the View|Layout options or their toolbar buttons you can switch between different types of showing the three files. By default all three files are shown, but sometimes it is useful to just see one pair of them, e.g. when editing.