Each insurance company has different methods for settling their total losses. You're stuck with filing through the other party's carrier, assuming they're 100% at fault. Your company won't be going after the other company because they can't collect anything if they don't pay for anything. So since you don't have collision coverage with USAA, they can't do much for you.
The company I work for uses NADA clean retail value. Other insurance companies have told me we overpay for totals, but we like to provide good coverage. That being said, your total loss settlement with the other carrier is negotiable. They can't magically make your Jeep worth more than it really is, but if they take deductions from the value based on existing unrelated damage, high mileage, etc. see if you can negotiate those deductions. Some companies may cut the deductions in half so that may help put some extra money in your pocket.
If they're offering you average value but your Jeep is truly in great shape, negotiate for a better value. Granted, the money you just spent on it doesn't increase it's value, they should offer you decent coin for a Jeep in good shape.
2012 KK Sport, Mopar skids, DuraTracs, Mopar Grille Guard
98 ZJ Laredo SE 4.0, 2" Skyjacker BB, JKS Quicker Discos, Goodyear Wrangler MT/Rs, K&N FIPK, Kolak cat & back exhaust, Westin Safari bar, KC lights