I got ARMA 3 to work! I can now exit play withSix and not have to redownload everything. Looks real good and thanks to everyone who put in the effort. Now lets see some MP servers fill up!
I'm not sure how I got it working, but I'm thinking it's because I didn't run ARMA2 at least once before installing the IF mod for ARMA 3. When I tried installing the mod for ARMA 2, withSix gave me a message saying I need to run ARMA2 before, I didn't get that installing for ARMA3.
After running all my ARMA2 and IF at least once, I then deleted anything @IF in my ARMA mod folders. I started up withSix and installed the modset for ARMA3. I noticed when the community patch was extracting, I have to click OK (didn't have to do that before). Everything loaded up and I can now see all IF maps in ARMA3 editor.