NIS is an Internet Security "Suite". It has anti-virus, anti-spyware, its own firewall and a lot of other security features. It runs in real time so it is not a good idea to use NIS and MSE or any other antivirus program together with NIS at the same time. It will cause a lot of conflicts and neither program will work correctly.
You can use the free version of Malwarebytes with NIS, use it as an on-demand scanner only, and it will work fine. Same with Spybot. You might be able to run the real-time Pro version of MBAM with NIS, but I do not know how well they might work together. You can set exclusions in MBAM Pro for NIS and see if you can exclude MBAM Pro in NIS, maybe they will work together without conflicts that way. If you decide to only use MSE you can run MBAM Pro without any exclusions, they will both work fine together without any conflicts.