The first answer is excellent.
Another point is - Use ModOrganizer - it will display the conflicts.
When you look at the conflicts you have a few choices. Quickest is to pick one mod to be the "winner" (usually by re-ordering your lists although there are more advanced mechanisms too). That's the most common decision because many conflicts will be things like a mod replacing an original Bethesda texture with something better. Another choice is to go look for compatibility patches. If there's no compatibility patch, another choice is to follow the ordering recommendations of the LOOT tool - but be aware that MO is one of the few tools that would allow the "loose" textures and scripts and other files to be in a different order than the LOOT driven plugin list of esps and esms.
And do what you're already doing - start with S.T.E.P. and think carefully about what you want to change.
And lastly - For stability, try to avoid removing or even upgrading stuff during a play-through. If you do, follow the "clean save" procedure on the S.T.E.P. troubleshooting page.
