It can take some work on your part, that's for sure.
Some mods can simply be added in, and nothing conflicts.
My mod folder starts with KHSM, then more is added. I have parts from the Star Trek mod, Babylon 5, and some special modifications of my own.
One thing to remember... things like the TechTree.xml can exist in two places. The one in the Data folder replaces the original in its entirety, while the one in the Data\Techs folder appends to the main file. Others that are like that include PlanetImprovements, Anomalies, StarbaseModules, CustomPlanets - basically any .xml that has a corresponding folder in the mod folder structure.