Emsisoft Anti-Malware is an Anti-Malware program, which is used to supplement and run alongside an Anti-Virus program. In general, Anti-Malware actually adds protection and helps with protection of the machine in addition to an Anti-Virus program. In general, Anti-Malware programs are compatible with Anti-Virus programs.
The act and effects of running Emsisoft Anti-Malware with an Anti-Virus program is not the same act and effects of running two Anti-Virus programs together. When there are two Anti-Virus programs running together, that is when problems can and usually do arise.
I realize that my knowledge (and thus explanation) is limited. So, you can read more about it here from a bleeping expert: here