A game that wasn't started as a metaverse game will be disqualified from submission to the metaverse. Any game that's updated after it starts, but before submission is subject to disqualification, so if you have an update, do it after you finish a game.
A cheat flag will disqualify the game, although it'll still submit. It'll just have a cheat flag on it and will show up as a 0 point loss.
A cheat flag will trip if you try to modify the game parameters after starting it or try to edit the score. It'll also trip if you complete the game before April 15 of year 0.
To anticipate what your question really means, I assume you'd like to know how to submit a game to the metaverse.
You'll need a Stardock.net account and a character set up for the metaverse. Once you set up your account, go to http://metaverse.galciv2.com/ and sign in. Mouse over the "Account" option on the bar and click "Edit My Characters" from the drop down menu. Click the "Add Player" button and add your new character. Keep in mind that if you try to input a character name that's already used, you'll get a strange error that might confuse you. It won't say to try another name. It'll say something else like your serial number is incorrect or some such thing. Try different names until it accepts one.
You'll then need to start the game in metaverse mode. When first starting the game, you'll see a "Metaverse" button. Click it and log into the metaverse. Select your character, set your game up and save it. You can use the quicksave button for convenience.
Once you've finished your game, you'll be asked if you want to submit it to the metaverse. The only time you'll see this option is if you started the game as a metaverse game. Otherwise, it's just a sandbox game.