Yes, in fact, that's the way it SHOULD be done. You should have a reputable virus scanner with up to date definitions and a good Malware scanner like Malwarebytes, both running real time protection. You should also occasionally do a full system scan as sometimes the RT protection misses something. In addition, it's a good idea to enable the Rootkit scanning option in Malwarebytes or use their free Rootkit scan tool from their website. Rootkits, Malware and Viruses are generally all mutually exclusive, being entirely different types of infections.
Virus scanners generally don't detect viruses and Malware scanners usually won't find traditional "viruses". Rootkits, adware and other undesirable infections may or may not be detected depending on what scanning utility you use. Always keep definitions up to date and when in doubt, use a "second opinion" scanner like Hitman Pro, which you can download for free. It nearly always picks up things missed by the other scanners.
I highly recommend the use of Avira free antivirus and Malwarebytes paid version, which is only about fifteen bucks for a lifetime license, used together.