Usually, manufacturers are able to panelize boards by themselves but sometimes it is difficult !
I have experienced a problem with panelization of 3 different boards (6+6+6) on the same panel.
Hopefully, I discovered on Hackaday the Gerber Panelizer tool, part of a suite of softwares called GerberTools.
And this saves me !
It is usable even if there are some little bugs. It also produce top and bottom realistic picture of the panel.
The main problem for me is that I do not succeed in building it quickly for Ubuntu, so I took an old Windows PC to do that.
To help doing what should be done, there’s also a big article about panelization on Electronic Design.
Hope all these information will help you in case of you fall there !
And maybe, all these tools can be incorporated in LibrePCB one day