Until you have a legal copy, you will not be provided support here. If you are not using a legal copy, then I would suggest you go get one: It's currently on sale for $40US, but is often cheaper during events, which the Spring Sale starts on May 23rd the Summer Sale on June 20th.
The fact that it isn't running and you're still running the game leads me to believe you're not using a legal copy of the game. In fact, MO2 does a check to see whether or not Steam is running when you run the game and if it is not, MO2 will attempt to launch it. Steam shouldn't affect anything, as long as you have a legal copy of the game, because the game is installed via Steam.
I've managed to launch the game and get it working from MO2 now through the SKSE launcher as long as steam isn't already running in the background but the mods aren't showing up. So they're both installed in separate folders in my C drive.
