Panelizing describes the process of combining multiple boards onto one panel for manufacturing. E.g. if your manufacturer's cheap standard PCB offer is for a 100x100mm PCB and you have two 100x48mm PCBs you can combine them into one PCB which you can later break appart. This seems like a easy to do thing, but the "right" workflow was pretty hard to figure out.
The general steps involved:
1. Finish a board layout on eagle
2. Export the Gerbers with the CAM-Files supplied by the manufacturer and move them into a folder
3. Check the Gerbers using a Online Gerber Viewer like [webGerber on mayhewlabs.com](http://mayhewlabs.com/webGerber/) or using a Open Source Tool like [gerbv](http://gerbv.geda-project.org/). Sadly both tools can (currently) just view Gerbers and not manipulate them.
4. For Panelizing there are strangly not many good open source tools available. After a long search I found the [pcb-panelizer by thisisnotrocketscience.nl](http://blog.thisisnotrocketscience.nl/projects/pcb-panelizer/) which has a beautiful and easy to use GUI, brings all necessary tools also in a commandline version and exports beautiful PCB-preview pictures while exporting panelized PCBs. Just drag the Gerber folder with the PCBs into the GUI and specify the panel size. Add Breaktabs.
5. Export panelized Gerbers
6. The panelized gerbers should be checked for possible errors (missing drill holes – maybe you imported both a .dri and a .txt drill file and he just used one?).
7. Upload to your PCB manufacturer's site
thisisnotrocketscience's pcb-panelizer allows also to save a file called .gerberset which can be used for future finetuning of a panelized gerber, without the need to import all Boards all over again.