To program a third party board you can use VISA Register Level Programming. The first thing you'll need to do is to generate an .inf file - this file is used for NI-VISA to properly locate your PXI instrument. To create this file, use the PXI Driver Development Wizard that ships with NI-VISA. This drivers will collect basic information about your board - manufacturer ID, model ID, and interrupt handling (if applicable.) Once the .inf file is created, you can ftp it to the RT controller. You will then be able to use VISA register level code (peeks and pokes, etc) to program the board.
Regards,
Dafna