US -
It is saying that someone is very, very stupid.
Is it hard to pour water out of a boot? (no.) if you can't do that, you must be dumb. It is even easier to pour water out of a boot if there are holes in the toe. It is even *easier* than that, if there are instructions on the heel of a boot, because when you turned it over to read the instructions, the water would fall out.
So, someone who can't do that is very, very, very stupid.
Also, the expression is usually "couldn't pour piss out of a boot." (it's a bit vulgar).