This should be pretty straightforward.
Simply goto your StreamTeam page, and click on Manage My Streams.
Choose the reach that you want to edit, and click on "Edit."
Near the bottom of the page, you can enter the newer, better lat/longitude coordinates for the putin and takeout. Click on "Add/Update," and you're home free.
Doing that for a dozen reaches or so can be a bit of a PITA. If all you're doing is updating a bunch of putin and takeout lat/longitude cords, maybe I can help. If you send me an Excel sheet (or other text-delimited file), with the columns arranged as follows:
Reach putin putin takeout takeout
Number lat lon lat lon
0000 44.4 -79.9 44.3 -80.0
9999 55.5 -119.9 65.9 -125.5
...etc., I can query the database and enter your coords painlessly.
(See all the rapids and campsites listed on the map in the Middle Fork Salmon? You don't think I entered all that data by hand, do you?)
Hope this helps,
Ratt