For months, seat assignments have been a major annoyance on mixed Continental/United itineraries. A CO-operated UA codeshare booked on united.com required that you copy the reservation reference number and proceed to continental.com to assign seats. The same was true of United-operated flights booked through Continental.
And even when seats were assigned, they did not always match up between the two sites. For example, upgrades on the United segments of my mileage run to Kona and Sao Paulo (that I am currently on) cleared, but the change in cabin and updated seat assignment was not reflected on CO's website.
Although the system still has many bugs, as of Thursday evening you are now able to assign seats on Continental and United flights on both CO and UA's websites. This should have been available a long time ago, but it is nice to finally see it. I am sure the reservations agents will appreciate it as well--one told me that more and more of her calls each day are regarding seat assignment confusion.
As I mentioned, at least on United's website, there are a few wrinkles to iron out. The seat maps are not entirely accurate and often misaligned. Even some of the UA flights are messed up--take a look at my São Paulo - Chicago seat map for Monday (and yes, I pan to upgrade):