Bootloaders Question for phyCORE®-LPC3250 Rapid Development Kit for WinCE

After erasing at least part of our NAND flash accidentally, I made some headway being able to use LPC3250 loader tool to have some ability to use Stage 1 loader capability to load custom NK.bin runtime images for our WinCE-based system. The info from Mr. Wells below was valuable:

http://www.lpcware.com/content/project/lpc32x0-cdl-boot-loaders/lpc32x0-...

I do have some questions, though:

1) I'm still a bit lost as to the exact way to load the stage1.bin and kickstart.bin files that came with our Adeneo BSP--so that they will execute completely without intervention of the LPC3250 loader tool. Just by rebooting the device. There are JTAG instructions with the BSP, but I am also hoping that we truly can do it completely through the serious port (UART5).
2) When I've tried different stage1.bin's, we lose capability, obviously. (Such as Active Sync.) I believe that from the info that have I read that the initializations are customized for kickstart.bin and stage1.bin--such as for including Active Sync or not. Is this true?

I'm stuck, and can use some help...

Thanks

rcsison