I am paying for my own truck but don't have my own LLC- I lease under a transportation company. The company provides a 1099-misc. Do I pay quarterly taxes like an owner/ operator, or just file the 1099-misc with my personal taxes each year?
The only actual tax return you file is the annual 1040 tax return. It will contain a Schedule C for your self-employment income. Even without your own LLC, you are considered as self-employed, selling your services to the trucking company.
If you owe tax at the end of they year, though, you can avoid penalties on underpayment of estimated taxes by filing quarterly estimated tax payments. This isn't a tax return, just a voucher with payments attached to it. As you complete your return in the program, near the end you can go through the Estimated tax payments interview under Federal Taxes, Other tax Situations to complete an interview for estimated taxes that will produce the 4 vouches you would need for payments towards 2018 taxes.
These vouches are not sent to the IRS when you do your return this year, they're just provided for your convenience in making the payments during the year.