I don't personally use or recommend mod managers, though I've seen a few people have success with both ModDrop and Vortex (more often the former than the latter). There might also some kind of silent majority that doesn't actually run into problems (or use very few, standard-install mods), but Stardew mods are so easy to install (unzip and put in folder) without any worries about load order and stuff that I feel like it's important to get familiar and comfortable with where everything lives before adding more layers. That way if/when something goes wrong, you can always redo it manually, no problem.
SMAPI shortcuts can be used to get basic "profiles" too, via
multiple Mods folders.
As for Content Patcher -- it's extremely well documented, so you can always
check out the docs! To add to Azrashar's comment, CP is not only a (better in every way) alternative to directly overwriting game files, but it also lets people edit only the parts of the files they are actually changing, which makes it much easier for them for multiple mods to stay compatible.
An example would be having a general craftables mod that recolors them all (and so replaces the entire file), a pack that changes scarecrows into kitties (only edits scarecrows), and a pack that changes the telephone into a, I don't know, giant clamshell. If all the packs are set up correctly, you can just use all three at once and all your craftables will be recolored except the scarecrows and the phone, which get applied on top and don't interact with one another at all.
It also lets you use do all that under a staggering number of conditions (like day, year, hearts with a villager, arbitrary configuration option set by modder, etc), which is how most NPC mods add so much variety to what are otherwise pretty normal edits to vanilla files.
(I think the mod you were thinking of was
Customize Exterior, which is still broken AFAIK.)
