Can I run Webroot w/ MSE?

It is not recommended to run two active anti virus at the same time.
They will fight each other and cause lots of problems.
I suggest only having one anti virus program installed at one time on one computer.
Malware and viruses are two different things.
A program I recommend for Malware is:
Malwarebytes : Malwarebytes Anti-Malware removes malware including viruses, spyware, worms and trojans, plus it protects your computer

or you could use the Professional version like I do.

https://store.malwarebytes.org/342/p..._free_page_top

http://www.malwarebytes.org/products...rebytes_trial/

I do use the Pro version on my home PC's because it is active protection that gets along with Windows 7.
You don't always have to go to a questionable site to get infected.
At times a normal website can get infected.

I can't tell you what the best anti virus program is. I don't know.
I can tell you what I use and it's works for me.

Microsoft Security Essentials
Malwarebytes Anti Malware Professional
The built in Windows 7 Firewall.
I also use Super Anti Spyware FREE on demand

When I run daily scans it's the quick scans unless I think something might of jumped into my computer.
I run complete long scans at least once a week.
I update all security programs a couple three times a day. It only takes a couple minutes.

Just remember Malwarebytes Anti Malware Professional does not replace your anti virus. It works along with it. Both active at the same time.

The Firewall is part of Windows 7.
Just go to the Start Orb and type in Firewall and you should see it. Just tick on it. (Firewall with Advance Security)
Windows 7 turns its own Firewall on as default as long as no other Firewall is installed.