First off, Logon Studio is old software for an old OS. It's no longer supported by Stardock.
To do the things you want to do with your logons, you CAN NOT use the Logon Studio editor to create the logons. All of the changes have to be done by changing the images in the logon folder and recoding the Uifile and Theme.ini. That is the only way you can get LS to support transparency.
And to get transparency in LS, the bitmaps must be 32 bit alpha blended bmps created in Photoshop or any other program that you can create them in, but Photoshop is the best one.
Then you have to change the coding in the uifile to accept 32 bit bitmaps. Any changes you make in the uifile will be changed back to default if you open them in the LogonStudio editor, so LS can only be used to apply them to see the changes you made and what you need to do to get it the way you want.
All bitmap sizes, font colors, and placement of the elements have to be done in the uifile. Fonts, font sizes, text are all done in the theme.ini.
A good place to get some info into coding the uifile is here: XP Logon Uifile Secrets
Towards the bottom, "Using 32 bit bitmaps for the buttons" will explain how to change the uifile to accept 32 bit bitmaps.
A tutorial for creating 32 bit bitmaps that will explain how to make them (it's made for creating bitmap 128, the center splash in the type of logons I create) but it will work for all the logon bmps is here: How to make transaparent "bitmap128" in Photoshop - An Article by pipowafu
That should be enough to keep you busy for awhile.
Hope it helps.