You can submit your taxes with $0 payment and then set up a payment plan for federal taxes (and state if applicable). Complete Steps #1-#3 to finish filing.
For Federal taxes, you can apply online to setup a payment plan for your taxes due (called an Installment Agreement) automatically, at the IRS website HERE. To start, click Apply as Individual. For more information on the process, the IRS has a video about setting up a payment plan HERE.
If you have state taxes due as well, google search, "your state + setup tax payment plan". You'll get some results about your state. Most states have a similar process.