I do not have navicore, but you can boot from either slot, any partition. You could then put the 1gb navicore card in the other slot. whichever "other" slot you want. There is a bootmenu.conf where you can change the slot or the partition number, you can even have a bootable card in both slots.

You should also be able to use say a 2GB mmc and have a 1gb bootable partition, and 1gb navicore partition and put say a 4 GB SD in the other slot.

You should also be able to boot from 4GB SD card, I just only have rsmmc available to test. I wonder which is faster mmc or SD? I want to wait for the 8GB to come down in price.