Say you have these match fields:
PlantSpecies::__pkSpeciesID = joinPlantReference::_fkSpeciesID
Reference::__pkReferenceID = joinPlantReference::_fkReferenceID
Then the following script will add a new record to Reference and also a correctly linked join table record linking it to the current record in PlantSpecies:
Set Variable [ $PlantID ; value: PlantSpecies::__pkSpeciesID ]
Go to Layout [ "Reference" (Reference) ]
Set Variable [$ReferenceID ; value: Reference::__pkReferenceID ]
Go to Layout [ "joinPlantReference" (joinPlantReference) ]
Set Field [ joinPlantReference::_fkSpeciesID ; $PlantID ]
Set Field [joinPlantReference::_fkReferenceID ; $ReferenceID ]
Go to Layout [ //you have two choices here, either plantSpecies or reference]
If the last step returns you to the PlantSpecies layout, you'll see a new blank layout. If there are a limited number of fields in Reference, you may be able to put all of them in your portal to the join table and simple enter the data in your portal--in which case your script can return you to the original layout or you may want the script to go to the Reference layout so that you can fill in all the needed details for that new reference record.
Fantastic! Thank you so much Phil, that worked perfectly.