The panel configuration file defines the source gerber files for each PCB, and specifies the details of the merged gerber output. Here is an explanation of some values you may want, from the SARduino644 panel configuration, which you can find in full here:
https://github.com/space-age-robotics/SARduino/blob/master/panel.cfg
# I always use the local directory to contain all input gerbers, config files, and output files
projdir = .
# MergeOut is the prefix of the output files.
MergeOut = merge2
# CutlineLayers will determine where the subboard markings are, which will help in separating them. These are the accentuated lines between the two instances of the board in the image below.
CutLineLayers = *topsilkscreen,*bottomsilkscreen
# OutlineLayers is used by the patched gerbmerge, it defines which layers the entire panel outline will be drawn on. Seeed requires this on all layers.
OutlineLayers = *toplayer,*bottomlayer,*topsilkscreen,*bottomsilkscreen,*topsoldermask,*bottomsoldermask
# here you can specify the maximum dimensions allowed by the Seeed PCB service you ordered (in inches).
# gerbmerge will warn you if your final panel (based on your layout) exceeds these dimensions.
PanelWidth = 3.93
PanelHeight = 3.93
# comment out the margins or set them to zero if you want the maximum amount of useable area on your panel.
#LeftMargin = 0.1
#RightMargin = 0.1
#TopMargin = 0.1
#BottomMargin = 0.1
# spacing determines how much space between the panels. I found 0.0625 to be plenty of space for a band-saw blade, I may reduce it a hair in the next run.
XSpacing = 0.0625
YSpacing = 0.0625
# if you define the merge output files to be in the filename scheme that Seeed requires, you won't have to rename them by hand later.
[MergeOutputFiles]
Prefix = %(mergeout)s
*TopLayer=%(prefix)s.GTL
*BottomLayer=%(prefix)s.GBL
*TopSilkscreen=%(prefix)s.GTO
*BottomSilkscreen=%(prefix)s.GBO
*TopSoldermask=%(prefix)s.GTS
*BottomSoldermask=%(prefix)s.GBS
Drills=%(prefix)s.TXT
BoardOutline=%(prefix)s.bor
ToolList = toollist.%(prefix)s.drl
Placement = placement.%(prefix)s.txt
# Job configuration - for each different sub-board, define a section like follows with the subboard name (used in the layout file) and the gerbers comprising that job.
[SARduino_644]
Prefix=%(projdir)s/SARduino_644
# List all the layers that participate in this job. Required layers are Drills
# and BoardOutline and have no '*' at the beginning. Optional layers have
# names chosen by you and begin with '*'. You should choose consistent layer
# names across all jobs.
*TopLayer=%(prefix)s.GTL
*BottomLayer=%(prefix)s.GBL
*TopSilkscreen=%(prefix)s.GTO
*BottomSilkscreen=%(prefix)s.GBO
*TopSoldermask=%(prefix)s.GTS
*BottomSoldermask=%(prefix)s.GBS
Drills=%(prefix)s.TXT
BoardOutline=%(prefix)s.BOR