I know what you're talking about, you're placing the jack where the rubber jack pad is located on the bottom of the car(directly undre the jack hole on the sideskirt). That's the only place you should lift the car from. Someone lifted my car up about a foot behind the jack pad and it caved in the floorboard, now my sideskirt doesn't fit quite flush
The problem you run into when you jack from there is that it leaves very little room to fit a jackstand, because the jackstand should be in the area where the floorjack is lifting the car. If you look a little further inward, you'll see two frame rails that run along each side of the transmission hump in the floorboard. I usually place the jackstands under those frame rails. You shouldn't do this, but if you do jack it up from the front crossmember, make sure you're not pinching any of the power steering lines and make sure the jack isn't resting against or hitting the steering rack. Just aft of the engine is another crossmember. This is what you replace when you install an x-brace. Do not jack the car up from this piece as it will certainly bend. I used it to jack my car up and it bent despite the fact that there is no engine in my car! No biggie though, I was getting ready to install my x-brace anyway. b.u.ti-ful is talking about an actual tool that plugs into the jack holes, providing an external pad to lift the car from.