I've found that the PC-BSD ZFS installer is kind of icky. It's unpredictable, and doesn't always quite do what you want. ><
But I guess that's the case with most GUI things, when you're used to doing it manually.
I'd recommend checking out the FreeBSD wiki for instructions on how to set up FreeBSD, and make installscripts.
If you want, I can give you my install scrips. Use at own risk, though.