My boot logo seems to have changed from the Empeg Car Audio (or something like that) to the penguin waving.
Do you mean that it changed from "Rio Digital Audio" to "Empeg" with the waving tux? If so, select the "File/Set Empeg/Rio Personality" menu in Logoedit.
is there a way to change how long the custom logo stays up?
No.
(Not exacty. But you can achieve the same effect.)
With Hijack and Jemplode, you can
customize the animated part of the boot (the Rio Digital Audio or the waving tux) so that it displays any frames you want. Some or all of those frames could be the same as your custom boot logo.