The way I've been doing the inlays in Easel is to run the app, then save a copy of the file, so I have 2.
Then call one the "Male" inlay (this will be the outline);
and call the other the "Female" (this is the fill).
I also find it helpful to add the type of material each piece will be, so if I'm doing walnut inlay in cherry, I would then have 2 Easel files:
• Project Male Walnut
• Project Female Cherry
That way I know exactly which one I'm carving out of which material.
Set the depth of the Female pocket a bit thinner than the depth of your inlay material. If your inlay material is .125", set the depth of the pocket to .115" or so. This will make the inlay sit proud of the face of the material, which you can sand flush.
You can set the machine up with both pieces on the wasteboard at once, then run the carve for each, setting the 0,0 point at the corner of whichever piece you're carving.
I wouldn't really recommend trying to do 2 species of wood or other material in the same carve, as you can't specify different feeds and speeds for them in Easel. You'd likely end up with one or the other part having some tearout or chatter, perhaps even breaking a bit if there's a big difference (ebony and pine, for instance).