Today I managed to configure IEI WAFER LX-800 board, the most important thing that the board has AMD Geode LX800 500MHz processor and 8 RS-232 port, it will also has to support PM-1028 multi-port PC-104 card.
The board has a configurable IO address at it's BIOS that need to be adjusted in order to make the PM-1028 work, so here the configuration.
WAFER LX2-800 IT8888 ISA Decode IO
Decode I/O Space 1 [Enabled]
Decode I/O Speed 1 [Slow Speed]
Decode I/O Addr. 1 [15:0] 
Decode I/O Size 1 [ 64 Bytes]
The 64 bytes size means that address range that PM-1028 used, the PCM-1028 multi-port module has 200H - 238H address range by default so 64 bytes will more than enough and it is the only option after 32 bytes size.
I also configure the PM-1028 multi-port to share one IRQ by using IRQ 5.
The Debian Lenny doesn't provide GEODE Xorg chipset driver by dafault. The package was named xserver-xorg-video-geode, without it the X server will fail to run no matter how the X configuration file is configured.