The taxes that were withheld will show up as payments towards the taxes due on the tax return. Just enter the 1099-R that you received as its shown and the software will do the rest.
Yea, but the penalties and taxes that I paid and considered income put me in a higher income bracket.
Yes, that happens. Pulling money from a retirement account is an expensive place to get the cash. If the 401K had been an IRA, you could have avoided the penalty on $10,000 of the withdrawal, but that doesn't work with a 401K. The entire amount is still taxable though.
Federal income taxes paid are not tax deductible. This means that the amount withheld for taxes from your TIRA distribution cannot be excluded from income. It's effectively the same as if the entire amount was paid to you and you then used a part of the money to make an estimated tax payment.