Balancing the plane upright or inverted will give you the same answer, however it may be easier to do inverted.

Work with the CG first unless you can determine the thrust line is way off the designers intent.

Look around for trim charts eg. [link=http://www.nsrca.org/trimA.htm]http://www.nsrca.org/trimA.htm[/link] and articles such as some found here[link=http://www.mini-iac.com/DesktopDefault.aspx?tabid=70]http://www.mini-iac.com/DesktopDefault.aspx?tabid=70[/link] for additional help.