FAB 3000 does have an easy-to-use graphical solution which Automatically Merges multiple gerber jobs. Essentially you load each set of gerber files into a separate job in Fab It!, the you create a Panel, and select the jobs (ie. set of gerber files) that you want to have merged into the panel. You can also define how many of each job you require on the panel. Fab It! will then calculate multiple configurations, and let you decide which is best.