Both distributions are considered to be income, but the rollover from the 401(k) to the traditional IRA is nontaxable income and does not affect your AGI or anything else on your tax return. Entered properly, you should see that the amount rolled over is excluded form the amount on Form 1040 line 4b and the word ROLLOVER will appear next to the line. With no other Forms 1099-R, line 4b should show $6,000.
