GPUDX mostly test plugin, have old GPU engine and a lot of incompletness.
If you want to get more quality image use GPUOGL plugin. It is more advanced (but have some bugs that DX haven't, fixing in progress) and with some flags combinations in config could show almost perfect graphics.
"List Sorting" used mostly for sort Transparent polygons that may be transferred to PVR unsorted and cause GPU glitches.
"Alpha Z-Write Disable" causes to not to write z-buffer for transparent triangles, but is just some hack so it may cause graphical glitches for some games (like Shenmue).
For most games best combination is "List"+"Z Disable" options enabled (RE:CV), some games perfectly works only with "List Sorting" enabled, other games looks better with all flags disabled but I'm not sure if there is one with perfect graphisc...
"Strip Explode" options takes many CPU usage but fixes some sorting problems, if you have wrong Polygons in front of others, use this option.
Capcom games looks some better than Chankast' ones, but you may play with "TMU timing" general option to make it faster (some sort of Chankast Capcom hack)...
If you have game hangings, try set "Period Update" option to 512 or 1024, some games need much IRQ latency, but some works only with 128, so it is default setting.
Pad configuration Dialog can bind any button on keyboard or joypads to any desired action buttons. But you should realise, that "PORT" option in "Bios&Plugins" menu set up DC controller desired to be insterted to "console".
"Controller" it is generic DC PAD, use additional port options to set VMU/VMS memory or Rumble to desired Controller.
"Keyboard" option means you want to use DC Keyboard as controller and of course couldn't be used for many games as controller since it needn't binding it uses exact keyboard pressings as input...