If an SCCM package installation requries a reboot, will the EEPO prevent the PC from coming up so the advertisement won't report back to SCCM?
I think you mean EEPC (Endpoint Encryption for PCs) - but yes, if you reboot a machine with EEPC on, it usually pops up the authentication page. To prevent this you need to use the "Automatically Login" AutoBoot policy option - this causes the machine to skip the pre-boot authentication.
It's not secure any more of course, but it lets you do your SCCM jobs etc. There's a lot of conversation on Autoboot here on the forum that you can read about, you can use automatic server tasks to schedule it etc.