Jeania, are you using a Mac or Windows?
I'm also not sure what you mean by splitting here and there. Could you attach a screenshot? You may already be doing this, maybe not, but are you attaching shortcuts to your program .exe's? On a Mac this is ok, but it's best to leave the programs in the application folder, on Windows, dragging the .exe out of the program folder most likely will disrupt things. I'm guessing you are linking to the files, you can easily check by going to Preferences, UI tab and checking the On drag and drop of files to Personalbrain dropdown. Also, I'm not sure if you are using Pro or Core, if you are using Pro you can add multiple links or files to the same thought, so you can have all the maintenance programs on the same thought. You can also put them under a Application, Maintenance Parent thought so they are all together (shown below). Hope this helps.
Java SE 6