then do i send a check next month for the balance and how will i know how much to pay in late fees

Yes, you would send in the remaining balance, unfortunately you won't know the exact amount but the following link has information on how to calculate the amount.  Any additional amount owed the IRS will send you a letter stating what you owe.
 <a rel="nofollow" target="_blank" href="https://www.irs.gov/businesses/small-businesses-self-employed/understanding-penalties-and-interest">...>
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You should also include the 1040-V payment form with your Federal payment
<a rel="nofollow" target="_blank" href="https://www.irs.gov/pub/irs-pdf/f1040v.pdf">https://www.irs.gov/pub/irs-pdf/f1040v.pdf</a>

The software will print one 1040-V.  Make a copy to pay with the second half.  If the first payment goes in now there will not be a penalty, just a modest amount of interest.  Don't try to calculate the interest, just pay the second half.  They will send a letter telling you how much interest you owe, later.

The software will not print a 1040-V form for the second payment, that is why I gave the link to the 1040-V.  As stated I said they would send a letter stating what they owe.  The link for the interest & penalty was for their information because they asked.