What we like to recommend is that you enter the first eleven prohibited transactions as normal. Then, on Line 12, enter in a sum of the remaining transactions that you will be placing on an attachment so that you get the correct calculation. Otherwise, you can always enter a sum of the prohibited transactions on Line 1 and create an attachment explaining all of your prohibited transactions.
Please click here to view the official IRS Instructions (scroll down to the "More than 12 Prohibited Transactions" heading) for additional information.