If you wish PB to start when you boot Windows, place a shortcut to the program.exe in your startup folder (I think this is the same in Vista).
In PersonalBrain, to to Options > Preferences and click on the UI tab. Make sure Show virtual Thoughts for folders is checked. Now find your desktop folder in Windows Explorer and create a shortcut to that folder in PersonalBrain (make sure when you drag the folder into the plex it has the shortcut icon before dropping it into the plex, if it doesn't, hold down ctrl+ Shift). You can do the same with your My Documents folder, or any other folder you wish to see in PB. Now below that folder should be a blue folder with your attachments, and child thoughts for each of the child folders. This way you can browse your file structure in PB. To make PB feel more integrated into your OS, go to the Window dropdown and make sure it's set to Float and maximize the window. You can then choose View > Presentation Mode (or alt + V then m). Then double click the plex background. To leave presentation mode, press the esc button. To go back to being able to view your tabs, double click the plex again. I have it set up so PB shows in my entire second monitor screen. If you set a nice (but not too loud) background instead of the default it makes a big difference. Anyway, just some ideas.
Java SE 6