The spindle, and the magazine/carousel are separate entities
You can put any tool in the spindle manually.
BUT,
if you wish to use the magazine, then a tool # must be applied to that tool, so it can be assigned/placed into a pot.
Lookup your machine operation manual, the section on tool management. It should explain the use of M6, M63, M64, oversize tooling(making adjacent pots empty to accommodate large dias).
Also how to change tool numbers of "loaded" pots
Hint... never fill the magazine AND have a tool in the spindle, it'll stop toolchanging in it's tracks.