"Unlike other malware protection products, a-squared Anti-Malware was designed to run parallel with other antivirus and firewall software without troubles. In case you find a conflict with another software, our support team will help to solve the problem quickly. "
source:
http://www.emsisoft.com/en/software/antimalware/
The real-time componnents include Mamutu and real-time scanning (not sure if AV engine is used).
If you want to try it, I would recommend to make a disk image first or at least a system restore point. You don't need to uninstall MSE.