I reallize that this post is several months old, but just in case anyone else is still struggling with the issue of refuelling aetherytes in particular:

As of the latest version of the mod at the time of writing, the item needed to fuel the aetheryte is Crystal Sand, which is unlocked with the Aetherytes research. You can craft 20 Crystal Sand with 20 of each type of aspected crystal (i.e. 20 fire crystals + 20 ice crystals + 20 earth crystals + ...).

In the item description for Crystal Sand, it says that it is "highly charged and used to fuel teleportation magic", but this is not listed on the description of the aetheryte itself, and the button to auto-fill it just says that colonists will auto-fill it with "aether crystals" (which is vague). Maybe this is something worth updating in the tooltips?

Thank you! I've not been able to play for a while but seeing this solved is a huge boon and will take this knowledge to the next time I play