Deep cut-outs?

One of my friends recently purchased a 3-axis CNC for woods/plastics and asked if I could help him out, because I mentioned I used one in uni for PCB milling so I'm a bit out of my element here. Unfourtanetly he is away at the moment and doesn't remember the actual machine name. I did see the machine and its a Canadian made one, large and well built, not a toy. I'm using Bobcad because he has a licence for it and drew up a part that I would like to test out on the machine, the part has U shaped cut-outs straight through, one is 1.4" wide by 2.875" deep and a smaller version of the cutout 400mills wide same depth,inner and outer radius are 0.125", I have flexibilty here if needed. The part will need to be flipped to do some protrusions on the other side. Would it be best to attempt to just do the cutouts from one side or to do half the depth on one side, flip it and do the other half depth? What would be the typical tooling used for something like this? The material is spruce for now but will eventually be a plastic for molds.

Thanks for taking the time to look. If this is in the wrong place sorry.

I'm attaching a pic with the larger cutout circled.