Will I have to repay the sign on bonus? They deducted all kinds of stuff from the check I received.?

The company and I had verbally committed to a one year agreement. The agreement I actually signed shows that I must pay back the bonus if I left the company within one year from the date the first commission check was received. I left one year from my start date so they got me on this.

However,
the aggreement states that the bonus was to be paid in the amount of 6,000 to the employee(me). They actually witheld 1000 to use to pay office rent and other business expenses.
Then they took out 10.5% to pay their payroll taxes.
So the gross check was 6000-1000-10.5%

Also, when I quit they decided not to pay me another 1000 I had earned in commission because I had not fallen through on the agreement.

Now they are saying I owe them the 6000 as signed in the original agreement.

What do you think?
Do I have to pay this back?

I was a W2'd employee. They always made me keep a $1000 account to pay rent and office expenses. I personally was never able to use this money.

The 10.5% was taken before my federal, state, and fica taxes were deducted from the gross check.

It was used to pay their payroll taxes. All companies pay them but usually you don't ever see it. It is their responsibility to pay payroll taxes as far as I know.

Verbal argeements don't hold up well in court but that paper one will.

You need to go over that contract carefully. Personally I would make them sue me. But if you do that then they may get compensated for legal fees, but you may win partially. The whole deal sounds kind of shady with you having to pay rent for your office space.

Was the 10.5% to pay taxes you owed on that money? How were you employed? Were you a contractor or employee. Work the contractor/employee angle and it may help in a legal case.