Anytime you dig out a bunker, which can sometimes take hours or hard work, you don’t want your hard work to get ruined with the first storm. So in order to keep your trenches in top form, I would suggest using a bit of forethought to keep them from filling back in or collecting large amounts of water.
To start with the best way to keep them from filling back in is to construct a retaining wall of sorts. What you can do is get some 2×6’s at the hardware store and lay them down on the floor of the bunker/trench. For the actual wall you’ll need some braces like rebar or metal fence posts of some sort, then make sure when you’re digging to make the walls slanting backwards so they fan out a bit. Then lay your 2×6’s accross using the braces to hold them in place.
Now that should keep the dirt from falling back in but what happens when it rains horribly bad and you’ve got a mini lake? Well to make sure you get some drainage you can dig out your bunkers so that they angle back and taper out so that the water has a channel to flow out of. To keep all the dirt from washing out of the bunker I would put some loose gravel or stones under your 2×6’s. If you wanted to get really fancy you could even get yourself some drain pipe systems.