I'm not familiar with Aldiko, and I'm sure there is some way to get the content into it, but at this time Calibre doesn't directly support Aldiko. There is an initiative to support it, but right now some donations are required to get the developer the necessary hardware.
Check here for info and links to chip in if you're interested:
https://www.mobileread.com/forums/sho...d.php?t=103690