why do you have drains in a sprinkler system? typically you put drains in a drip system. are they used for winterization? if it is for winterization, you can accomplish that by adding an entry point for compressed air and blow out the system once per year (beginning of winter). can you remove and cap the drains?

Dig a larger sand well.

When using the autodrain elbows, you should dig a large hole under the head, and refill with peagravel or sand. This gives a place for the water to accumulate after the zone shuts off and slowly percolate into the soil.

If your soil under the head is not absorbing the water, removing the drain would be a better solution than making a second puddle.