Say, making a texture atlas is only graphical work. You need a program which can work with layers. Then free program can be Gimp for example.
You put all smaller parts on one texture (document/work area/image howerer you call it) - keeping them on layers allows you to make corrections much more easily. At the end - flatten the image or merge layers and save as dds (or jpg) - remember that the texture should be in "powers of 2" (2x2, 4x4, 16x16, 32x32, 64x64, 128x128, 256x256.... and so on).
Texture atlases are good solution when you want to use less materials - many objects can use the same texture, which makes the same (and only one) material for all of them.
Then it's a matter of making new objects (in Sketchup, Blender, 3dMax or other programs) - all of the objects will use the same texture atlas.
Merging the materials has to be done in XPacker (he always adds new material any time you add new object to the xpack). If you don't know how to do it, I will write about it here later.