You can use animation frames rendered from a 3D package to create 2D sprites in Unity as long as those frames have transparent background. Combining those frames into a sprite sheet saves precious draw calls (sprites are treated as one texture) and makes your game run smoother on lower end devices. It is also easier to organize your project files if you combine sprites into sprite sheets. Unity can automatically split a sprite sheet with transparency into multiple sprites. It recognizes empty pixels (transparent pixels) and isolates individual objects (or animation frames) quite effectively.

Unity can also automatically pack the sprites into a sprite sheet using the sprite packing feature. To pack sprites into an atlas, first make sure that packing is enabled. To do so, go to Edit | Project Settings | Editor and check the Sprite Packer Mode. You should change it to Always Enabled. Then select the sprites you want to pack into one atlas and give them the same Packing Tag. Finally, open the Sprite Packer (go to Window | Sprite Packer) and click on the Pack button. All sprites with the same Packing Tag will be packed together.