ITYT's got a great mileage calculator for US airports that can handle up to two connections and allows you to specify the minimum number of miles that any segment will receive.

For example, with Continental's Onepass program, set it to 500 miles and you won't have to manually add in those miles. However, other airlines have varying levels of minimum mileage awarded, so you can change it accordingly.

Much quicker than the Onepass site and supports airports that Continental doesn't fly to, in the off chance that you have to fly non-CO.

http://www.ityt.com/mileagecalculator/