To set up people picker to look for accounts in more than one domain you have to configure the Peoplepicker-searchadforests stsadm property. Take your time reading the documentation as it seems to be a little bit unclear.

Before you run the stsadm command you have to run the following command (if you are entering credentials to connect to the domains)

stsadm -o setapppassword -password <value>

This will be used to store credentials for the domains you query in the peoplepicker. If you don't do this you'll get an error message when you execute Peoplepicker-searchadforests.

Here is an example on how to configure peoplepicker to read from a domain with a one way trust and a domain with full trust

stsadm -o setproperty -url http://myserver -pn "peoplepicker-searchadforests" -pv "forest:trusted.domain.org,trusted\user.name,password;domain:my.domain.com"