"... and then have a good travel agent you can book your tickets through as you want them booked to maximize miles/segments?"
Booking via a travel agent won't work - CO
only gives 50% Elite Qualifying Miles and 0 Elite Qualifying Segments on deeply-discounted fares not purchased via continental.com.
The best way to book a complex segment run:
1. Pull up the routing rules using expedia - go to flyertalk.com under the mileage run forum to figure out how to do this;
2. Look up the skeds on continental.com to determine what connections would work;
3. Book the flights 1-2 segs at a time on continental.com - for example, I booked my segment run as BWI
4. If the fare isn't what you expected, call continental.com customer support to have them manually reprice your itinerary into the lowest possible fare class.
5. Get ready for one hell of a segment run!
Live life to the fullest.