General: Create your objects with a surface on Z=0, not layered above. This will set everything to usable g-code pathes.
Created tools will end up on your file system within your </path/to/tool-library/>/Bits/ Tools that are stored on other places will not be saved when modifying your library.
This job will hold all your operations. On this level you will select the body to work on, the tool to use etc.
spindle speed: 9000
horiz. feed rate: 3mm/s
vert. feed rate: 1mm/s
To create a pocket choose "Path" --> "Pocket Shape". Select the bottom of a to-be-created pocket and click on "add" in the base geometry dialogue.
You need to make sure that depth are fine (stepping is, for whatever reasons, set to tool diameter instead of something that makes sense).
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Path --> Post Process
The generated file can be used as input for example in Universal G-Code Sender.