Where do I put the prepaid interest charges on my Closing documents, if they were not added to the 1098?

The only way to enter it is as if your received a 1098 form. Do select 'add a lender' then enter the interim interest you paid on your closing documents in Box 1 interest.

Other Items on closing disclosure form that may be deductible:

• interest paid at the time of purchase (the charge at closing would normally be done for interest up to the date of first payment). 
• real estate taxes charged to you. 
• points - On a refinance they need to be amortized over the life of the loan; unless the points were used to improve your main home.

Other fees, such as commissions, attorney fees, preparation of deed, abstract fees, owner title insurance, recording fees are added to the basis of your home, and not deductible.

https://www.irs.gov/pub/irs-pdf/p936.pdf