Automatically by code or simply with Paint and some definition file with the regions (in xml for example). You can also create an atlas fixed sizes and generate the coordinates.
For example an 512x512 atlas can contain 4 256x256 textures, and you generate the coordinates programatically. Then you store the information in an array and paste them right in an your texCoordBuffer.
vertices 1 -> texcoord 1, vertices 2 -> texCoord 2.. and so one, like you would normally do with 0 to 1 now with 0 to for example 0.5 from the texture. You just need to calculate where the coordinate start and end.