If your main focus is real-time detection and BB/HIPS (zero-day protection components) then it would be very wise for you to keep Emsisoft Anti-Malware installed on your system as your primary protection (with both the real-time protection for the file system and the Behaviour Blocker enabled) - without that being said, apparently the Malwarebytes Web Protection is really good and therefore you could always keep this enabled for the real-time with MBAM (and disable it with Emsisoft products).
If you experience any conflicts you can attempt to resolve them via white-listing the other product from the white-list settings (on both products), or opening a support thread on the vendors forum/website [
Emsisoft Support Forums,
https://www.malwarebytes.com/support/]
I did some searching for you to check if there had been any responses from Emsisoft/Malwarebytes themselves about the compatibility and I found a few links for you to read:
EAM Compatibility with Malwarebytes Anti-Malware - Emsisoft Anti-Malware
Malwarebytes Anti Malware compatible with Emsisoft Anti Malware?
Please read this quote from GT500:
Technically Emsisoft Internet Security isn't considered compatible with Malwarebytes Anti-Malware due to the fact that Malwarebytes Anti-Malware uses a WFP driver to capture network traffic for their website blocking, and that driver could cause problems with the WFP driver used by Emsisoft Internet Security.
I am unaware if this is still the case or not, however if it is then it seems the Emsisoft Internet Security firewall won't be compatible with Malwarebytes Anti-Malware if both of them are working with the web protection. (and it may be the same case with EAM as well).
You can test out both products to see if you experience any conflicts. However, you may experience additional noticeable performance issues depending on your system... If you do experience a slow-down I recommend disabling Malwarebytes Anti-Malware for real-time protection and keeping Emsisoft Anti-Malware real-time protection enabled (since I believe that Emsisoft is more reliable and will provide more detection's overall - without that being said, every vendor has it's good and bad days and no product can detect 100% malware).
Honestly, I recommend you just follow the suggestion
@Spawn gave where you can use Emsisoft Anti-Malware/Internet Security as your main AV suite (since it is designed to be a full AV suite, it was re-named to "Anti-Malware" since the engineers felt that it would fit the product better) whilst using Malwarebytes Anti-Malware as an on-demand scanner alongside (you can even set-up scheduled scans with it).