There were 3 separate check-in areas for Economy, Premium, and Upper when I was there this week, the Premium and Upper check-in areas were on the kerb / entrance side of the building, opposite the main Economy check-in. There are also a few machines you can use if you don’t have any bags to check.
There were Virgin Atlantic signs saying check-in opens at 2pm, so about 3.5 hrs ahead of the VS92 at 5.25pm that I flew on.
I concur with Kraken, avoid the left two lanes of Precheck.. I made this mistake and found out the hard way! Allow plenty of time anyway, as all of the lanes are slow, and sometimes they just stop altogether for 5 minutes as the cramped scanner area behind them gets clogged up.