I am not quite sure how to ask this question, but I guess whoever has been there before might give me his advice.

While working on big assemblies, I initially used sub-assemblies in order to group parts and lessen the number of items displayed on the feature manager tree, while later I found folders as an alternative way to do more or less the same.

I understand sub-assemblies let you add constraints between different parts while folders are "only" a logical arrangement, meaning that parts are not constrained necessarily between the parts of this folder directly, but might be constrained to other parts in the main assembly. 

This difference becomes very much alive when noticing how many constraints disappear when creating a sub-assembly.

Moving parts between folders behaves quite straightforward, while moving parts between sub-assemblies requires a different work.

In our field of work (refrigeration) sub-assemblies are most of the time rather arbitrary, because when heat exchangers are involved there are by definition two different circuits that part belongs to.

Moreover, "group" suppression (either a sub-assembly or a folder) are possible , though hiding is only possible for sub-assemblies, and you need to select every item in a folder if you want to hide them.

I hope I made my point clear. I look forward to hearing some else´s approach on how to keep things organized when assemblies begin to get big enough.