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use Installer to install rSBT. now use rSBT to put those icons and any others you might prefer under the 'Hidden' section. Now they should be gone from your main screen.
I am also having a problem deleting an app I put on manually not using Installer. It's like iphone remote and it has a question mark for the icon but it won't let me delete it using Fugu...I'm on a mac too