It will run fine with Defender. I've got it on 3 machines using Defender.
MBAM was designed to work in conjunction with AV software.
And with 3.0, Malwarebytes is actually touting MBAM as an antivirus replacement, but you can still run AV software. If you want to, go ahead. More layers of security is better, so long as they don't nullify each other. But I plan on sticking with Defender and MBAM 3.0, and not running flash and java.