Anything that is flat (i.e. stratus) you can just fly through. Convective clouds (coughulus) range in size from puffy little things, to huge monsters. Little doesn't matter, but it's generally a good idea to at least strap everyone down for a larger one. If it has lightning, then don't enter it if you have any choice at all. Convective cloud will have vertical motion, and that's what gives you the bumps.
Oh, and contrary to the media, the atmosphere does not contain 'air pockets', nor do aircraft that encounter turbulence 'drop thousands of feet'. Imagine what driving over a plowed paddock would be like at 100 kph...you only need a foot or so to make it very uncomfortable. A really huge bump might drop the aircraft 10 feet, but that will be more than enough to throw those would don't like seat belts all the way to the ceiling, from where they will fall back onto whatever/whomever is below.
The air isn't homogenous. There are layers, and they often travel at quite different velocities and directions. Normally, in the middle of a layer it will be smooth (which is how we can use jet streams to dramatically increase the ground speed on the Perth - Melbourne flight), but anywhere near the junction, where the layers mix, the air will be rougher. Climbing or descending, even as little as a thousand feet, can often get you clear of the boundary and find smoother air.