Rather than using the running total expert, you are going to have to do it manually. What you need to do is create two Global variables (one for each year) and use an If statement to assign the proper value to each one (summing it as you go along). Something like this (you'll have to modify it - I'm just typing off the top of my head).

Global NumberVar Total2006;
Global NumberVar Total2007;
if Year({table.datefield}) = 2006 then
    Total2006 := Total2006 + {table.amountfield}
else
    Total2007 := Total2007 + {table.amountfield};

Then in the report footer you can put formulas which print each total or print the differences.

Global NumberVar Total2006;
Global NumberVar Total2007;
(Total2007-Total2006)/Total2006;

I have three chapters covering writing formulas and building manual running totals in my Encyclopedia book. You can find out more about my books at Amazon.com or reading the Crystal Reports eBooks online.