I think you're unable to change the sprint logo because the flip clock actually brings the logo image with the clock. Not sure if I read this wrong though. I was trying the manila file as well with the flip clock and it doesn't work. There's a thread around here that explains how to change the logo on the flip clock but it's a different process.
EDIT: Ahh not the thread I was looking for but i think it's the same guy... I haven't tried this but I guess you need to rename the "443d5315_manila logo, just rename that to 29ed4fb5_manila and use it instead."
Source:
http://forum.ppcgeeks.com/showthread...ing+flip+clock
Check post #6
Of course you need to edit the original manila file in manila editor with the logo you want.