I received a 1099 for nonemployee compensation. But I have deductions for the full amount that is taxable ( I got $800, I can write off $900 ). Do I have to fill anything out or just keep records of my expenses?

Yes, you can do it but chances of audit by IRS are high.
Generally, no one will work as independent contractor if the job related expenses are more than the income except in a few cases like Adsense income.

Well I was receiving another source of income as an employee at the same time, so my expenses for my nonemployee and my employee were the same, and was basically getting paid twice for the same job. In an overview I sell cars, and the manufacturer gave me bonuses that were 1099 as nonemployee, but I was still paid from the dealership as well. So my mileage and other such deductions became greater than my income from the manufacturer, but I was still making income reported on my 1040. Any advice?

Yes, you can do it but chances of audit by IRS are high.
Generally, no one will work as independent contractor if the job related expenses are more than the income except in a few cases like Adsense income.

Well I was receiving another source of income as an employee at the same time, so my expenses for my nonemployee and my employee were the same, and was basically getting paid twice for the same job. In an overview I sell cars, and the manufacturer gave me bonuses that were 1099 as nonemployee, but I was still paid from the dealership as well. So my mileage and other such deductions became greater than my income from the manufacturer, but I was still making income reported on my 1040. Any advice?

I am not exactly sure we are talking about the same thing here, but if you receive incentive payments from an auto manufacturer while employed by the dealer, those awards/bonuses are reported as Other Income on the front of the 1040 and not on Schedule C. Any related deductions to generate the awards go on Schedule A as an employee business expense. The awards are not subject to self-employment tax.