Thomas,
There are a couple ways to do this. Depending on your end product configuration, the easiest thing to do would be to write a Lolo script or 2.

The setup could be a new card engine, put the card engine into an SDK that is already hooked up to ethernet and has a Compact Flash card in the CF slot that contains any software you want to put on the new card engine.

When power is applied to the kit, Script1 is sent to the card engine over the serial port. Script1 could mount the CF card or connect to a TFTP server. Typically you'll want the script to load and burn a different version of Lolo from a TFTP server or off the CF card, then load and burn a winCE or any other OS image to onboard flash. The script can then update the CPLD code (typically not necessary unless you have custom code for your product).

Depending on your needs, the Scripts can also be used to do functional type testing in the final product.

LogicPD can help with the script creation process with a small support contract if you find you need help beyond what the forum provides.