If you want to do trenches, then you have to do them properly which might mean spending more than a little money on them. A good, proper and long lasting trench system is far more than just a hole in the ground that is longer than it is wide. Line the edges with sandbags to mark them for safety, and consider putting some as bunkers with structured roofs over them.
Think about where you put holes in the ground, as they WILL gather water. Dig them a little deeper than needed, and fill the bottom with drainage tiling and crushed gravel. Pack the side walls, structure with sandbags, and reinforce with corrugated sheet steel if you can. (All edges safely capped) If you design the bottoms of your trenches as drainage ditches that actually lead somewhere they can drain into, then you shouldn't have many problems.
For any structures I would plan them out as a small village or work camp. Lay them out on paper as you would expect to find in a real world, non-combat situation. Then while building consider what quick impromptu fortifications that could be done to them.