I would think that if the tank was stationary, not moved or sloshed around, any water entrained in the fuel would drop to the bottom of the tank. Therefore, not using the very bottom of the tank would probably insure you that you wouldn't get any water into your trucks system.
A good fuel additive, like Stanadyne, that separates the water from the fuel may be helpful. It may, also, help in preserving the fuel, long term.
If you had a way to filter the stored fuel before you put it in your truck, that might insure that you remove any algea and its byproducts that may have formed in the fuel.
You may want to go to a website called "bob is the oil guy.com" & post that question. There are some pretty sharp people, over there, some of whom own companys that sell products to the fuel industry.
Joe F. (Buffalo)