Now about your adding in new mods and where they should go. MO will inform you of a conflict but it makes no judgement on whether one mod or the other should win, that's up to you.

'Conflicts' are not necessarily a bad thing.

if the conflict is shown in the left-hand pane then it has nothing to do with the plugins. that MO shows are specific to the panes they are in.

The messages/colour coding/icon flags/etc.

Regarding MO's UI and how conflicts are shown. So the game loads the whole overhaul, it's assets, scripts etc first then the game then gets the call to load X, Y and Z based on any plugins they provide. (Like you have a Meadery with it's own glassblower, say.) You would likely want any plugin from that Mod to load before the plugins from our three example mods above. So to keep going with our example, suppose you have a mod that allows you to actually craft bottles. They do various things, but one things they do do is tell the game what to load and when. Ideally then You'd install X first, then Y, then Z.

Z just does new bottle labels, which are better quality than X or Y. Y is a specialized mod that uses the meshes in X but adds extra texture details to the Booze bottles. X is a complete overhaul of all bottles in the game. As an example you have three mods X, Y and Z. This has ramifications on what may 'win' if you have two mods that do the same or similar things.

Install order: Order in which your Mods are installed.

Mod organizer 2 vs nexus mod manager