Ashton D. said:

Would I just do a journal entry to fix this?

Yes, that is the easiest for you right now to finish the reconciliation.

Ashton D. said:

Can I reverse the payment in Sage and then re-do it with the changes without it causing issues?

If you want to go this route, I would not reverse it, I would just adjust it but you said

Ashton D. said:

Sage won't allow me to revise the payment to deduct the .01 cent

So you need to figure out why it won't let you adjust it.  You have not indicated any error messages that came up when it prevented you from looking up the entry and hitting the adjust button so we cannot help much.

However, the easiest way to get rid of a pennyish different between invoice totals and short payments is to enter the difference in the Discount column.  You must put the discount in before the final amount paid.  So enter the penny in the discount, hit tab and the final payment will calculate for you.

You do have to have a linked account set up for discounts in the Setup of the program and I know some company files do not have this set.  Check Setup, Settings, Receivables, Linked accounts to make sure you have an account set up if you cannot use the Discount column in the future.