First as long as you have water coming up your patch probably won't hold. When I want a good seal in cases like this I do it in the summer when the ground water levels are lower. I believe hydraulic cement is the proper type of material to fill these holes, many times if you can plug them water will start coming up in other locations.

Allowing the water to flow through the patch will reduce the risk of someone getting hurt because of the hole but I would plan to do the repair in the summer if trying to seal. A couple of holes will allow the water to flow and not push the plug of new concrete out. Water underneath is not the problem, it's the pressure. They pour bridge footings under water, once the concrete displaces the water and fills the forms, it cures and works fine.