While figuring out my 2006 Estimated Tax, I came across this issue.

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I Worked under 1099 as an indepedent contractor late in 2006 in U.S. which is where I live. The first pay check was manual check from the company I worked for, and the rest from the company's payroll company. I'm trying to computer my 2006 estimated tax to send it out before 1/16/07 deadline. My problem is on the final paycheck stub, the payroll company did NOT include the amount I was paid for by the manual check, and I was told by the company I worked for that I can just use the number on my final paycheck stub to figure out my Estimated Tax. This number does not include the 1st pay, manual check. I think the payroll company probably has reported IRS whatever the number was on my final paycheck stub which doesn't include the amount on the manual check. What do I do? Do I use the number on the final paycheck stub OR add the amount of manual check to the number to figure out my 2006 estimated tax? (To clarify, 1st check was a manual check, and from 2nd check it was direct deposit processed by the payroll company. My 1st paycheckstub (my 2nd pay) shows the amount starting from my 2nd pay, and never included amount I was paid