No such guide exists, I'm afraid, and none likely will be. Modding in Skyrim is such an involved process that simplifying it to the level you'd like is not really possible. To really do it well takes time, trial and error, and then more time.
That said, a few things I've picked up that are relevant to your original question. Keep in mind I've never tried a SRLE install, so can only speak to how STEP Extended is laid out and implemented.
1) When looking to add additional mods, try to place them (roughly) in the same general category as ones already installed. An an example, placing mods that alter NPC appearance in the 'Characters and Creatures' section, or things that change game play systems into 'Gameplay'.
2) As part of the above, when placing them, use MO's conflicts tab (double click the mod, conflicts tab) to make sure that the stuff you want to make sure is there isn't overwritten by a mod further down the load order. The Flags MO uses can also help you identify when any mod becomes completely redundant (white lightning bolt), which means you can likely remove it from your load order completely.
3) Understand that Skyrim is kind of like a cat. It hates you. It has no real plans to work with you. It will randomly, and with no real rhyme or reason it seems, work or not depending on it's mood. Random Acts of Skyrim are to be expected. Sometimes, there is a reason, but it can be a pain to track down... don't lose your focus. A little research can help out with these problems, and the guys here will (and have, on many occasions) help you out as best they can to figure out possible causes of problems. Just stick with it through the frustrations, and when it finally gels and you get that awesome Skyrim look and play, it'll be worth it.
I know it's hardly a comprehensive list, but like anything with this many complicated and interwoven systems, it's a beast to make into science. If you have more specific questions, I'm sure I (and the others) will help out, but at a general level, that's about all I've got.
Good Luck... we're all counting on you.