If it's a longer species you will probably want something deeper.
A good rule of thumb is to do as much substrate to millipede length.
So a 3 inch species should have at least 3 inches of substrate.
You don't necessarily need holes if you open the container every couple days.
I have both tubs with and without holes. I just make sure to pop the lid open on the one with no holes every other day and it does fine.
So it doesn't really matter either way.
If you do decide to do holes, just make sure they're small or in the lid so the millipedes can't manage to climb out!
If those are Sterlite boxes, I have found them to be very brittle and often crack when I drill. Like SlugPod said, you really don't need holes in these. I like Hefty High Rise boxes the best. They drill cleanly and are roomy. The most common size I use are the 32 qt., which is 17LX12WX14H. Have fun!