Water in fuel

[Still Hunky Dori]

We ended last season being towed back to our marina. Mechanic told us that there was water in our tank and that both separators were full. Before the boat was winterized, they removed the remaining water from the tank. After launching the boat last month, the engines again stalled while in our slip. Separator filter were again filled. Took the boat out after emptying the filters and again both engines stalled. This time the fuel filters were clogged.

Should I continue to run the engine and check/empty the separators as needed? Or should I have the boat hauled out and the gas removed from the tank?

Is there any relationship between the water in the fuel and the gas filters be clogged?