@komatthew 

"Since the deposit can from the CD and its going to the CD."

I think you missed this part:

@FishingForAnswers nailed it:

"and a spot to select the account the money is sourced from (Interest Income, probably a column named Account)."

You need to select Interest Income under ACCOUNT (below 'Add funds to this deposit'), not the CD.  The CD is selected under Account in the upper-left corner of the deposit screen.  If you select the CD under ACCOUNT, it will decrease the CD by $2,194.12, which is what you're seeing. 

That will increase the balance in the CD by $2,194.12 and increase your Interest Income by $2,194.12.