One of the payments will be for the remainder of any tax that hasn't been covered by the two estimated payments on account you've already made for 05/06, the other will be the estimated first payment on account for this year.
Ring up and get them to sort out a time to pay agreement, and as long as you stick to it you'll be OK, not sure you'll even be charged interest - ask when you ring them.
Alternatively, if you know that your current years profits will be lower, get someone to estimate your tax bill and reduce the payments on account. Only problem is, if you end up underestimating the tax, you'll owe interest on whatever the difference is.