It's a little tricky, but you can do this if you don't mind having a Status Item (aka Menulet) for BookMacster.

• Click in the menu BookMacster ▸ Preferences, then General.
• Check the box Show BookMacster status in menu bar.
• Check the box Launch in Background.
• In your Bookmarkshelf window, click Settings ▸ Open/Save.
• Make sure the top box, Open this document when launching, is checked.
• Quit BookMacster.

Now, whenever you launch BookMacster, it will open your Bookmarkshelf but it will be a "background" application.

• Launch BookMacster.

Now, the Bookmarkshelf window will never show, although the Inspector will, depending on whether or not you hold down the option key.  (The option key behavior has a preference too, Preferences ▸ Adding.)

When you need to really get into BookMacster,

• Click the BookMacster status menulet in your menu bar.
• Click Show BookMacster.
• Activate any other app using the Dock or ⌘-tab.
• Activate BookMacster using the Dock or ⌘-tab.

The last two steps are due to a bug in Mac OS X which I see that, sadly, Apple has still not fixed in Mac OS X 10.7.1 despite repeated reports.   Another unfortunate "feature" of Mac OS X is that "showing" a background app is a one-way operation.  Once you have clicked Show BookMacster, the only way to get it back into the background is to quit and re-launch BookMacster.

Also, check out the Status Menulet and consider using that instead of the Bookmarklet to add bookmarks.  Sometimes, it takes about 10 seconds to load the first time you click it, but it allows you to traverse your hierarchy and add bookmarks wherever you want to.

Maybe this can be made easier in a future version.  Let us know what you think.