To clarify, you can have Malwarebytes run when you start your PC but real-time resident protection is only available in the paid for version. So, unless you are starting the program with the intention of running a scan, then all that having it running in the background is doing is taking up your memory and wasting CPU cycles.
Best thing to do is just run a quick scan once per week, and if it finds anything, run a full scan afterwards to be sure there's nothing else. More often than not (and hopefully) it won't find anything.