disabling the popup is fine so long as you don't disable that actual protection to get rid of the annoying messages!!
it will really depend on what you are doing as to how often things will kick into action...
network virusses are usually worms, that will compramise your computer, install an EXE file and then start that exe file, your virus scanner is finding that process once it is running, and then removing the EXE?
whilst a virus scanner is a great start, you should also consider a firewall. (outpost is a good one available for free from http://www.agnitum.com/download/
you'll also find that some websites you go to will have active content downloaded into temp and your virus scanner will warn you that there is a virus in the temp folder as well.