Use tripod and some kind of remote, either the laptop or the wired remote, which ever.
I would use the 50mm, not sure which extension tube combination will give best results but I would try a few combinations until you get the subject within the the full frame and still have some focus tolerance on both sides.
I would use aperture priority mode starting at about f16, shutter speed will be determined automatically but if you find the shoots over or under exposed simply adjust your exposure +/- setting accordingly. Remember aperture controls DOF and ultimately how much of the subject will be in focus, shutter speed doesn't really control anything related to detail provided everything remains perfectly still.
Manual focus as previously discussed, focus on the center point of DOF on the subject to maximize overall DOF. Mirror up could be a good idea, but again but if your tripod is decent you shouldn't need it. Mirror up may be automatically selected if you're using a laptop with a live preview.
Remember to set the WB, minimize ISO, and shut off all tank movement and room lights.
For blacking out the background experiment with smaller apertures (remember that means higher f number) and longer exposures. You may notice that the background becomes darker but it's pretty hard to completely black it out with the camera only so you'll have to finish it off in photoshop.
You can do it completely manually as well using photoshop by making multiple layers and using the quick selection tool.
