By 'good faith' money you're most likely referring to 'earnest money'. The earnest or good faith money is applied towards your down payment on a home you purchase. If, for example, you are applying for a VA Loan (Veteran's Administration) which typically does not require a down payment, your good faith money would be used towards any other costs you would typically incur at the closing.
You should speak directly with the Loan Officer who is handling the financing for your property. He/She will be able to give you a very detailed account of how the good faith money will be applied so that your questions are answered correctly for your exact situation.
Congratulations on your purchase in Kentucky. I hope your experience is flawless!