Sorry, ignore the bit about the dll. I was thinking about the 3booter and fpslimiter.
Anyway, as long as the mod folder is in your base game folder it should work. Are you using the Beta or Alpha version?

Make sure it is the right folder. Also make sure the .cfg and the .dll files are in the right place.

I've been having some problems with Supreme Commander. My two sims were on Work and School, but 90% of the time they ran to the fire station to play foosball. I deleted the table, causing them to find a second one. After deleting that, too, the ran off to play on the fire station computers, even though they had their own laptops. This happened even if they had full fun and Having a Blast moodlet. Other supreme commander tones had a 10% chance of pointless gaming. So unless there is an Addicted to Computers trait I don't know about, something is wrong.

Everything else seems to be working fine; no crashing or freezing.

The red flag in your first post was "overwrite." If you put the expansion in Sims 3/EP01, then you won't overwrite anything and probably won't have any problems.

Short answer: no.
Long answer: noooooooooooooooooooooo.

Do not install WA in the original Sims 3 directory. You will probably break your install if you do that. There is a reason it defaults to a different directory.

I just got a FSE trying to travel to china, but it's letting me keep playing after I clicked the check mark.

Edit: The game is now stuck on the loading screen for China.

I just recently turned on Supreme Commander, and so far it's pretty useful. It could use a couple more options, though. Socializing and/or Family Time. What good is a better AI if the sim's wife is indifferent and his toddler is starving on the porch. I guess I can sum up my request in two parts.

1. The option for a sim to call people, visit houses, chat online, and just plain talk to family members.
and
2. The option for a sim to Potty Train, Teach, Read to, Feed, and otherwise care for their children.

Looking foreward to more Awesomness!