You can put your Jeep VIN in the PCM just fine, be warned when you go to use the Scan tool you will not have any enhanced or DMA PIDs because these are model specific and become active when you connect to a GM vehicle. With a Jeep VIN, EFILive will think the PCM/ECM is not a GM one and therefore not load the PIDs.

Long story short, get it running 100% using whatever VIN it comes with then change the VIN once you're done tuning.