No, just create your model and its UV's like you always do. The only extra work you need is connecting the images to the nodes, which usually can't take more than 2 minutes.

If you decide to use the texture atlas mode and you don't have the texture with the proper requirements, you need to create an atlas. Check the FAQ below for more information. This still doesn't require any additional work on your model.

No. The textures need to be aligned on a grid with even spacing and dimensions. For example if you are using a 4x4 grid, you can have exactly 16 variations and you can't make one variation take, for example, two slots.

The easiest (and probably fastest) way is to import all the images as planes (using the "import images as planes") addon. Scale and position them evenly on the grid then render the image.
Note: Make sure to use an emission shader on the materials, and don't use Filmic for rendering to keep the colors accurate.