I believe that last pic was 1/125, 5.6 and 400 for the values. I can check it with the canon program.
ahhhh......theres your problem. f/5.6 is waaay too small (i.e. aperature is too big), thus the reason why your depth of field is so small. and the picture is too dark probably b/c your shutter speed is too fast.......if you have your f-stop to around f/9-f/13, in Av mode the camera will automatically adjust your shutter speed depending on the available light...but it should set the shutter speed somewhere around 1/4 sec, thus allowing in more light....but to do this you need a tri-pod, and the pumps must be off.
these are the settings i use on my Canon XTi for macro pics:
-Av mode (dial on the top right of the camera)
-set f/stop to f/12 (normally take macro pics at f/9 to f/13). the higher the f/stop the greater the depth of field
-ISO 0 to 200
-exposure should be set to 0, make sure you don't have yours set to -2 Ev/Av
-make sure you are shooting your pics in RAW format
-Auto White Balance usually works just fine
-user the self-timer funciton....so the camera counts down from 10sec before taking the picture.
-make sure the lens is perfectly perpendicular to the glass of the tank
-make sure all pumps have been turned off.
-make sure you are shooting on a tri-pod (important when shooting in Av mode b/c the shutter speeds are longer).
-also, if you know how to set the custom functions.....make sure to turn "long exposure noise reduction" to ON, and "mirror lock-up" to ON.
also, make sure to set the lens to manual focus......and focus the lens manually yourself instead of letting the camera do it.