Hi @MLanger,
Welcome in the Community !
The situation you describe looks like a Two-way Split Plot experiment : a first step involving specific factors create batches, and then these batches are randomly applied with new factors from a second step process.
To create this specific design with the Custom design platform, the factors from the first step should be set as "Very hard to change", and the factors from the second step should be set as "Hard to change", with the option "Hard to change factors can vary independently of Very hard to change factors" checked (if you want to randomize applied factors from the step 2 in regards to step 1) :
Note that you can modify the assumed model, as well as the number of whole plot and subplots to your convenience and experimental budget.
You can find an example and explanation on how to setup and analyze this type of design here : https://community.jmp.com/t5/JMP-Sample-Data/Design-of-Experiments-Example-A-Two-Way-Split-Plot-Expe...
If you need more details, help or guidance, you can provide more info on the number and type of factors, your goals and assumed model, etc...
Victor GUILLER
"It is not unusual for a well-designed experiment to analyze itself" (Box, Hunter and Hunter)