Retirement tax questions

I think I am looking too much into this. Since it is pre-tax, would the pretax amount already be calculated in Box 1? For example, in this case, if the Gross Income is $30,000 but during the year the 401 (a) pretax contribution was$5,000, should Box 1 state $25,000?  I ran a summary before I printed my W-2s, in QB, and in this case $30,000 was listed as total gross pay in the summary, and $25,000.00 was listed in Adjusted Gross pay after the pre tax deduction (401 (a)). But when I issued the W-2's earlier today Box 1 was $30,00.00, and in my eyes, maybe should be $25,000 after the pre-tax deduction? Otherwise wouldn't you be paying taxes on it now and then when you take it out later on in retirement, therefore double tax? I have the 401 (a) listed as NONE in my Payroll item list since it is not listed.