MSE should be your virus protection, MalwareBytes freebie only being run when required. If you have the pro (paid for) version of MalwareBytesit probably runs in the background. In which case you must decide which one to use for this purpose. MSE would be my choice.
If you have an icon for MSE then open the program and ensure that in the Settings tab you are ticked for "real time protection". See if you can get updates too.
If you have no MSE icon you can either open it from Start/All Programs, or copy this into the Run box and hit Enter:
C:\Program Files\Microsoft Security Essentials\msseces.exe
I think that once you get MSE working as your primary virus checker there is every chance that you will be able to click it up in CP/Sec Center.
If you can't get MSE to work at all then uninstall it, download a new copy and install that.
Long Range Golfer