Endpoint Protection SBS 2013 Cloud questions

Why do we have to uninstall Malwarebytes to install and run SEP SBS 2013? Malwarebytes should be able to co-exist.Until SEP finds and removes everything Malwarebytes does, I still need it.

2nd question is how do we adjust the cloud client to add exceptions and tell it to only scan programs files, etc? My clients are complaining that their PCs are much slower after removing Microsoft Security Essentials and installing SEP SBS 2013. What can we do to speed things up?

Thanks,

Dale