As long as your code is in a parsable directory (such as mysite/code/*) then SS will include it (or you could include a require_once 'File.php' in the class that requires it).
If you extend the class off object you do get access to a bunch of nice SS stuff like extensions and static stuff but note there is a performance hit when extending from object. We noticed a large performance gain when skipping this extension from classes which didn't require it.
Double-A-Ron - Yes any directory or sub directory of a folder with a _config file and no _manifest_exclude file will be included in the manifest. I am pretty SS the manifest builder should pick up any PHP classes regardless of what it extends as long as the ClassName == Filename you should be good.