As you haven't provided any specifics, such as where your real-time clock is (which cell or cells does it display in) and what your VBA code is actually placing in a cell or cells, it's pretty difficult to provide an answer.
In general terms the difference between two times in say cells A1 (time now) and A2 (finish time - a time in the future) is A2-A1. If the formula A2-A1 is in cell A3, then formatting it as [h]:mm will display the time difference as hours and minutes even if the difference is greater than 24 hours (i.e. >1 day)
Next you need to consider whether the time now and finish time are either both times only with no date information or both time+date information, or one contains time + date and the other contains time only.
If both are the same, then the simple A2-A1 formula works.
If A1 is 11AM today and finish is 11:30AM tomorrow the difference is 24:30 using [h]:mm format.
If A1 is 11AM on 11 August 2010 it stores the value 40396.4583 (approx.) , even if formatted as hh:mm
If finish time in A2 is 12:00 (entered by typing in 12:00), it has a zero date and holds 0.4792, and thus A2-A1 is negative.
Use this to get the decimal/time part of A1 to compare with A2: =A2-MOD(A1,1) - which compares times only and the difference 11AM on 11 Aug 2010 and 12:00 is 1:00.
Finally as you are doing a count down you need someway to stop a negative result, once you get to zero, the result needs to remain zero.
With Excel times, if you have A2-A1 and A1 is later than A2 you will get a cell filled with ######.
So use this in A3: =IF(A2<=MOD(A1,1),0,A2-MOD(A1,1))
If you need more help, please provide details of what you have done, and include the VBA code that creates your times.