I have used xcircuit to draw my charts and then load the graphics into lyx. It works very well, not only for the flowcharts but anykind of simple drawing.
For drawings, which are not too complex, PSTricks is a good choice. See
http://members.aol.com/Mluque5130 http://melusine.eu.org/syracuse/pstricks/ http://www.pstricks.de/examples.phtml
Herbert
