First, let's cover importing your Delicious bookmarks always into the Bookmarks Menu.  If this is not working for you, first, remove bookmarks from the Root if there are any.  Then in the Structure tab ▸ Items Allowed at Root, uncheck "Bookmarks".  Then at the bottom set Default Parent to Bookmarks Menu.  Now when you import from Delicious, all bookmarks should go into the Bookmarkshelf's Bookmarks Menu.  Worked for me.

Next, regarding Import Clean Slate not applying to the Bookmarks Bar, BookMacster does not allow such granularity.  It's either all ON or all OFF.  To get the effect you want, you'd need two Bookmarkshelf documents.  The one in your screenshot would become your "DeliciousToSafari.bkmslf".  It would have all the Clean Slates ON as you have.  Then you'd create another Bookmarkshelf which would be your "Safari Bar.bkmslf" which would have items in its Bookmarks Bar only.  This one would never import, only export, with Clean Slate OFF.  Workflow would be something like this:

• Activate DeliciousToSafari.
• Import.  (Clean Slate is ON)
• If there are new items you want moved into Bookmarks Bar, move them into the Bookmarks Bar of the other document, SafariBar.
• Export.  (Clean Slate is ON)
• Activate SafariBar.
• Export.  (Clean Slate is OFF)

I believe this will do what you want, except that items you deleted in the Bookmarks Bar in SafariBar.bkmslf would not be deleted in Safari's Bar.  The Activate, Import and Export steps can be scripted.  Import and Export can be scripted by setting up triggerless Agents and telling them to 'perform' via AppleScript.

Now if you would instead do your deletions in BookMacster instead Delicious, then you wouldn't need the Clean Slate on Import, and then you'd only need one Bookmarkshelf.  That would be a more normal usage for which BookMacster was designed:

• Import new bookmarks from Clients
• Sort, Move, Change, Delete, Verify, etc. in BookMacster
• Export final result to Clients

Regarding tags in Safari, remember that BookMacster keeps the tags.

But I probably have not appreciated all the nuances of what you want, so that's enough for now.