I just started using 6.4 yesterday, but anytime i add a map entity in WED it won't show up when i run the game. I feel like its something incredibly simple, i just can't figure out what. Any input would be appreciated.

Check Preferences under File menu, and see if Show Entities is checked.

Hmmm, Not sure if this still happens with 6.4 anyways the last version use to change the file name sometimes when you opened it and append ~???? something to the end of the file name.... When you build the wmb will have that new strange name. Which means if you try to run the level it runs the old wmb file and not the new one. So check to be sure that the proper saved name is in the top bar when you open your level. If it does have ~ something written at the end simply go to open and open your level. It seems to mainly happen when using the dropdown list of previously opened levels. So opening your level thru the open dialog box should fix it. Hope im making sense here.