I have a standard I use for myself when installing outside the STEP lineup. For starters I create mod categories that are exactly the same as what STEP has, it makes for an easy way to see mods from STEP are all installed and in order. Also I very much like there mod category labeling. So if you look at the mods they have in each category most speak for themselves, you should be able to understand what they mean, well they do in fact define their categories somewhere in the guide. So taking this knowledge, I then do my best to try and duplicate that for a non STEP mod, and install it where it seems more likely. So if it's a new armor or weapon, it would go into clothing and equipment. I place them in alphabetical order unless install order is important, just like STEP does. And so on and so forth. But keep in mind, as with modding in general, it will be trial by fire, unless of course you adhere to a strict STEP mod lineup, where they have done the trial by fire for all of us. Other things to bear in mind is how one mod might affect the mod's inside STEP, specifically, what options, if any, are chosen during the installation. What do I mean by that, well, I myself use mods, that another mod used in STEP has a a patch for compatibility, but since the mod is not inside STEP, naturally STEP tells you to install what is necessary for a STEP install. So, you will need to remember during installation, if any options are necessary for a mod you are adding outside of STEP. A good example off top my head for a mod like this would be AOS (audio overhaul for skyrim). AOS has MANY compatibility patches for mods, and while STEP only uses a few patches. Also STEP provides compatibility patches when there is not one available by the authors, So, you yourself might bring a mod to the table that may conflict with another, and compatibility will need to be addressed. And that is a very advanced stage of modding.
Wow, that wound up being longer than I had originally thought, lol. Anyway, I will stop with that for now, that's plenty food for thought at this point I believe. Good luck and happy modding!