No, you can go ahead and pay online. The IRS will receive payment and credit it to your account. This will not confuse things as long as payment is received
Since you are not paying with the e-filing of your return, you will have to arrange a payment. If you pay from your bank account, no fee is charged or you can pay with a credit card that includes a processing fee.
Please see this Pay Now article from the IRS to arrange payment.