If you have PCB's that are 2 dense and or small for tooling holes you can have an ATE jig made for the whole panel and have the tooling holes on the panel border. I have done this in the past. Where ever you put the tooling holes you will have to provide some information for the jig to be made. To have jigs made in the past I have sent Gerbers, mechanical drawings and ODB++ data, with the latter being the preffered format as it is the simplest to produce and provides the most comprehensive data.