You're talking about two different things that could both be known as "deductions." First there are deductions from your paycheck, like your 401k contribution and your withheld taxes and your insurance premium. You can set up your own deductions in Employee Express. They're called "allotments" in that system. I have a deduction/allotment going to my Roth IRA, and another one going to a separate savings account.
Then there are deductions from your income that you use to reduce how much income you pay taxes on. The "standard deduction" is one example. Contributions to a traditional 401k are deducted from your income, as are contributions to a traditional IRA if you're eligible. If you lost money in the stock market you can deduct that amount. That sort of thing.
It so happens that the FAA knows trad 401k contributions are deductible from your income, so they go ahead and reduce your per-paycheck taxable income by that amount and withhold taxes based on the lower amount. That's nice. They don't have to though—if they didn't do that, you could take your 1040 at the end of the year and put down how much you contributed, then deduct that amount from your gross income.
I don't believe there is a way in Employee Express to set a user-defined financial allotment as pre-tax, that is to say, to tell the FAA to ignore that amount when withholding taxes. I could be wrong. I would recommend calling HR and asking. But it doesn't matter at all. If at the end of the year you're eligible to deduct the amount from your gross income, go ahead and do that (you'll get the withheld taxes back as a refund). If at the end of the year you aren't eligible to deduct the amount, no harm no foul, taxes were already withheld.
I feel like I'm taking crazy pills here...
