The general rule of thumb is that if two mods change the same thing, they will conflict. Now, that doesn't always mean you can't run the two together. For example, if you like what Skyrim Flora Overhaul does for grass and flowers, but you like the trees from Enhanced Vanilla Trees better, then just make sure the Trees load after (below in the list) the Flora.
Scripted mods will be more of a problem. So, it's wise to read the mod description thoroughly. Apocalypse and Phenderix's Magic are surprisingly compatible because basically what they do is to add new spells to the game, along with the appropriate spell books. However, The Path of Sorcery will require a patch to work with Apocalypse so that the perk changes from Sorcery apply to the spells in Apocalypse. The author of Path supplies the link to a patch for Apocalypse in a sticky post on his Comments tab. There doesn't seem to be a patch for Phenderix's Magic.
Mods which change the same places in the world will conflict with often bizarre and sometimes game crashing effects. Expanded Towns and Cities will conflict with Holds - the City Overhaul. There's nothing to do but choose one of them, which one is really a matter of personal taste. Settlements may conflict with ETaC, I didn't check ETaC's map that closely.
Your best source of information about conflicts is always a mod's description. Read those descriptions carefully and take notes if you need to. I will confess that I usually just skim the list of things that are added, such as spell lists, but I read everything else thoroughly. If all else fails, check the Posts and Comments tabs.
Good luck with your modding adventure. Remember, save early and often!