How to split configurations in features to minimize conflicts
What I try to do is to build up features in layers. At the bottom most layer you put all the things that do not depend on anything else in your features, such as contrib modules, site settings and the like.

At each layer you add features that depend on the layer below, trying to avoid cross-dependencies. Each feature should be as standalone as possible apart from its depndencies on lower-level features.

It's difficult to achieve perfection, though, because a new feature may affect things you have already configured. For example if you install the field permissions module for a specific need, that'll add extra settings to fields you have already configured. So that module effectively becomes a dependency of sorts even though logically it isn't.