Well, I've only uploaded a logo once (the original Rio Car logo to replace the Hijack logo) and didn't have any problems as far as I recall.
First make sure you have you logo saved as a 4 color, 128 x 32 pixel bitmap (.bmp) file. You will need a photo editor program to do that. Then use Tony's Log Editor and choose "File" and then either "Import Home Image" or "Import Car Image." Point to you logo file, and it should show you a preview in the editor window. Your choice depends on which mode you want the logo to show up. If you want the same logo for both modes then do it twice, once for each mode. After you have your logo(s) previewed in the editor window, choose "File," "Send boot logos to player on com(x)." Follow the instructions on the window and your logo(s) should be installed.
Stu
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If you want it to break, buy Sony!