When I tried to use scriptaculous and Atlas in the same .aspx page, I saw that scriptaculous methods (for example Ajax.Updater,Form.serialize) does work correctly correctly.
I find out that Atlas has its own $() function which is overridden the scriptaculous's own $() function.
One ugly but quick fix is to rename $() function in scriptaculuous to something else like $$$(). But remember to change all references in scriptaculuous scripts to use this function.
A good solution seems to be remove $() function in Atlas as $() function in scriptaculuous is doing the same and a bit more. but I dont know how to modify Atlas script(actually I dont want to change it).
Maybe someone has a more elegant solution?