We've been running it for some time now without any issue. I would start here:
https://isc.sans.edu/forums/diary/Beefing+up+Windows+End+Station+Security+with+EMET/18107
EMET and SEP will run in tandem as two great layers of defense. We've used it to protect against vulns to MS office products, outlook, java, adobe, IE...
SEP was never considered in configuring EMET as they should have no impact with one another. EMET protects against software vulnerabilities.
Per it's doc:
Are there restrictions as to the software that EMET can protect?
EMET can work together with any software, regardless of when it was written or by whom it was written. This includes software that is developed by Microsoft and software that is developed by other vendors. However, you should be aware that some software may not be compatible with EMET. For more information about compatibility, see the "Are there any risks in using EMET?" section.