Bill -- Numerous members have the program called WIN1010 by K4HAV and that will track the counties for you. It also does EVERYTHING else you can think of for 10-10 as far as any of the awards goes. WAS, mobiles, CW, PSK, countries, etc etc.... Another program which I believe may help with counties but I'm not totally sure is N3FJP's program -- I'm not as familiar with that one ---
Also, go to the following URL: http://www.ng3k.com/Misc/usc_ind.html
That will give you a listing of all the counties by states --- If you have a spreadsheet, some people utilize that method if you know how to keep track of counties and not duplicate them.. There are ways of doing that --- Also, check with the Counties Award Manager and see if he has any other info for you as well. Most all of the individual Awards Managers are more than willing to help you out with any questions you may have. Also, you can put your question out on the Ten-Ten list service and the TenMeters Group Listservice and you will get many ideas from lots of members who have done this or are doing this and also many different ways to track what you are collecting. I hope this helps some.