An extroot replaces both /rom and /overlay with a writeable (usually ext4) filesystem on the external drive. The files in the internal flash are accessed only during boot until the extroot is mounted. During the process of setting up an extroot, the entire existing filesystem with your configuration and installed packages is copied to the external drive.
A package is basically a tarfile. The files it contains will be placed in several places in the filesystem as appropriate. Typical locations are /sbin (binaries and scripts) /lib (libraries) and /etc (configurations). With internal flash, any additional files added under / are in the jffs /overlay. With external root they are simply in the ext4, merging with the copy of /rom made when the extroot was set up.
The opkg files command will show the files installed by a package and their location. The package must be installed first.