Thank you for your interest.
In order to add imported products to correct websites, please check appropriate websites during import:
http://screencast.com/t/lyHAqhhY
If the issue with displaying products at correct websites remains for you, please provide us with your store connection configuration (you can save it at Preferences[F12] / Actions / Save current configuration), import configuration (you can save it at the last step of import wizard), .csv file via e-mail (not here sine it is a public forum) so we could check what caused the issue for you.
Waiting to hear from you