Is there anyway I can restore certain files if I use the backup from the server-manager page?
What backup are you referring to. Backup to desktop. Backup to tape. Other?
The server-manager does not provide for this so the quick answer is no. The real answer is anything is possible if you visit the command line and manipulate your backup manually. However this requires a very high level of knowledge to get it right.
This is the main shortcoming of the server-manager backup procedures and why alternate contribs exist.
Darrell