Is it better to use CIA or 3DS files for citra?

im confused, and new to this

Depends on the type of file. Any ROM files should be dumped as either .3ds (for cartridges) or as .cxi (for installed titles). However, any updates and DLC should only be dumped as .cia. So that they can be installed. Our dumping guides explain how to do all this:

Dumping Game Cartridges
Dumping Installed Titles
Dumping Updates and DLC