This is actually a major part of my job, dealing with malware.
I wouldn't touch MSE for several reasons.
A. It's common, too common, especially for noobs, this means it's a ripe target.
B. You have all your eggs in one basket, I.E. Microsoft, who has a history of being sh*t when it comes to stopping malware. You have them handling your o.s. security, your av security... No. Diversity is good.
C.
http://www.neowin.net/news/microsoft-security-essentials-fails-another-antivirus-testThe only thing I have seen it do well was deal with a rootkit. However, it required making a disk and blah blah blah... Tdsskiller did it in a quarter the time and without a boot disk.
As for what to run, frankly most malware is coming in through web advertisements. In fact the last survey showed only 3% was coming through email and no single approach will stop it all (well, almost).
I have well over 300 systems running this setup, including my own, it's a multi-pronged approach, however, it's relatively low in resources and all of these programs are free(!). Anything I work on, ends up with this setup (unless they recently bought something like Norton) and the business owners and I try in earnest to make sure nothing gets on their network without being checked first as most have seen the results first hand. In fact, that is usually why I get called in the first place.
Level1
Run an adblocker. Adblock Pro for Chrome, and Adblock Edge for Firefox. This blocks 90%+ of the junk out there.
Level 2
Winpatrol. Winpatrol is a VERY low resource program (uses only 3megs of memory) that most of the time sits idle. Every few minutes, it simply scans every autostart location in Windows. It keeps a list of approved programs, and if something new pops up, it simply asks you if you want to allow it. It's a much better version of the U.A.C. If YOU are careful, this program alone is the best anti-virus program there is, and is probably the only pro-active one on the market (rather than reactive). My brother and I went 6 months with only this and an adblocker and never caught anything despite being careless. In fact it was so good, I was worried about losing my business if I installed it on customer computers. I didn't need to worry, people are always the biggest threat.
At this point, it's pretty much only user error that allows the system to be infected, which is why...
Level 3
Avast Free. I have Avast Free running. This is their basic protection, I absolutely hate firewalls (biggest con job the anti-malware industry has put over on the general public, topic for another discussion) and "internet protection" packages. This is mostly to protect from anything I download or comes through my network.
If I suspect something has gotten through, that too has a multipronged approach.
First is Tdsskiller, this removes rootkits.
Second is ComboFix, this takes care of 90% of the junk you will get.
Third is Super Antispyware
Fourth is MalwareBytes.
After this, I uninstall all of these, then run CCleaner to clean out the temp files and the registry.
At this point, the system should be squeaky clean.
If I do have something I suspect is flakey, I run it on a system I use a sandbox system.
