When you assemble the kit for a unit, you need to build units with unit cohesion in mind.

When I build a unit of models, I make a model to fit with the models it will be standing with. Then I label the bottom of all my models with their coordinate position in the formation they were built for. (1a,2a,3a,1b,2b,3b,etc)

If you just make a bunch of models in cool poses, then try and rank them up after the fact you are going to have the most frustrating experience of your life.

As far as charging into one another, you should try not to have spears and things pointing 3 inches out, but really units don't need to physically touch each other.