When you bought the Expedition, you paid retail, now about $5500. If you want to trade it in, you'll only receive wholesale or "trade-in" value, about $3000-3300 depending on your negotiation skills. So there's a difference, or spread, of about 2200-2500. So if you put less than that down on the Expedition, then yes, you would not receive in trade what you owe on it.
If you are determined to sell the Expedition, then selling it privately would bring a better price - especially if its got 4WD and you're looking to sell in a snowy area. This would be a good time to sell a 4WD vehicle privately in the Phil. PA, southern NJ to DC, No. VA, MD etc.