There are instructions elsewhere about this, but things are a lot easier on the WACO because both wings are shaped the same. Just use the average distance from the LE of the tail to the LE's of the wings. In other words, if one wing is 4 inches ahead of the other, and the most forward wing is, say, 25 inches from its LE to the LE of the horizontal stabilizer, you would input (25 minus 2 inch = 3) inches from LE to LE. (Or you could use the distance to the least forward wing and add 2 inch in my example.)
Then input the length of the wing as the TOTAL of both wings. For that, if the top wing is 60 inches (30 inches half-span) and the bottom wing is 58 inches (29 inches half-span) then you would input (30 + 29 = 59 inches Half-Span). This little trick will get the proper answer for you. The other way to do it would be to use the average half-span, but tell the program you have double the chord of a single wing. Either way, you need to tell the program enough to calculate the total wing area that includes both wings.
Using these methods, you could calculate CG for a Fokker Tri-plane also.
Just remember the program will give you the distance to the CG from the imaginary "average" Leading Edge, so remember to add or subtract the input distance (2 inch in my example) when you are marking your CG. It wouldn't help for me to measure my WACO because it's 1/5 scale and does have a 60" top wing. sorry.

Hope that helps.

"The AC location for biplanes with positive stagger (top wing ahead of the bottom wing), is found according to the drawing below.
[link=http://adamone.rchomepage.com/index5.htm]http://adamone.rchomepage.com/index5.htm about 3/4 down[/link]
For conventional designs (with main wing and horizontal stab) the CG location range is usually between 28% and 33% from the leading edge of the main wing's MAC, which means between about 5% and 15% ahead of the aircraft's Neutral Point NP."