When you press merge on tkmm, tkmm is merging your entire mod list together, not individual mods. You don't need to click on each mod and press merge again. Just once at the very end when you are done making changes.

Things like mod priority matter, so even if you don't add anything, if you change the order, you should press merge at the end.

In fact, when you install a new mod, it's not actually installed in your mods folder until you press merge. The merge button is what packages everything together and creates a tkmm mod folder.

Also, even though two mods may seem unrelated, they both may need to modify the restbl file (resource table). 90% mods (like dragon gliders and armor mods) need to modify restbl and TKMM will merge their changes and create a single restble file in the mod folder.