Just getting into CNC-- need basic help

For something like this I would not recommend you use a CNC (Mill or Router presumably) but rather a Laser (likely CO2 or perhaps blue diode). CO2 lasers work well on anodized aluminum (though not at all on steel, non-anodized or other metals unless you get creative).
The (from me recommended) process would be to use some wood, plastic, foam, etc. to create a cutout where you can place each part and then manually/visually define where to engrave (plus maybe some way to account for height). That would be very repeatable (maybe +/- 0.01in) and fast too (that's the kind of process I've used on multiple projects).
However, if you do choose to go down the mill/router path, the approach is similar: you need to set up tooling that allows you to consistently define the location. This can be as simple as a vise with some indexing feature or as complicated as custom plates that contain some way to mount the parts. Question is one of number of parts and how much tolerance you can live with...