You can put FFmpeg and the other utilities anywhere you wish. Just make sure that when you configure pyTivo it has the proper path for them.I'm installing the wmcbrine version. It says to extract the .zip to a folder of your choice referred to as the <install folder>.
I used C:\program files\pyTivo (I'm running XP SP3)
It says to put ffmpeg and tivodecode files in <install folder>\bin\
When the wmcbrine .zip was unzipped it created a folder in the c:\program files\pytivo called wmcbrine (c:\program files\pyTivo\wmcbrine) with several subfolders under that folder.
Should I put ffmpeg and tivodecode in c:\program files\pyTivo\bin\ or in c:\program files\pyTivo\wmcbrine\bin\ ?