If you search the file section of the forum you will find an Amel drawing of the fuel tank for a Super Maramu that will help you understand what the internals of the tank look like. The drawing apparently is not 100% exactly as built, but it is close.
If your tank is contaminated with water, you can extend a tube down the fill pipe to reach the deepest part of the tank to pump it out with a hand pump.
After enough time, even the cleanest diesel tanks accumulate hard, black "coke" on the bottom from the slow, unavoidable, oxidation of the fuel. When this breaks loose it can cause all kinds of problems. As far as I know the only way to clean it is to mechanically remove it.
I did this on my old boat, cutting holes in the tank, and using these to patch them up again:
Be really, really careful cutting holes in the tank. This might be best done by an experienced professional. Diesel fuel and fumes are not very flammable, but a mistake can cause the tank to explode. I know someone who came very close to dying when this happened to him!