About installation order... there's 3 types of installations
Mods that use esp/esm/bsa files
Mods that use lose files
Mods that use a combination of both
Lose files will always have precedence over the same files placed in esm/esp/bsa archives, so in case of conflicts they will always win. What you need to understand about load order where there are no lose files involved is that lower placed mods win over higher placed mods. This is great actually because it gives you a logical order to follow: BIG to small
With that I mean that if you install Overhauls (lets say - weapons) you can start with big packages first and make sure that if you have other smaller mods that replace a certain kind of armor/weapon load them after.
Eg. I have a mod that replaces all NPC armors for a more detailed one, and lets say this with with an .esp file. Now I have another mod that changes just the Dark Brotherhood NPC armor, also in an .esp file... I would want that loaded after my bigger overhaul so it will win the conflict (it will obviously have one). This is of course only for conflicting mods... If you are in a situation that no mod conflicts then really, just put them somewhere, it really doesnt matter a single little bit... but hell, everyone is running 50+ mods, so that situation doesnt really exist anymore.
Usually I follow the following
[Official ESM files]
[Other ESM files from mods]
[Unofficial Patches]
[--Here would go things that say to load directly after USKP]
[Race Compatibility]
[SkyUI, iHud, RaceMenu, etc but not Character Maker Extended!]
[Static Mesh Improvement]
[Landscape Texture Mods]
[Landscape texture, smaller mods (rocks, etc)]
[Flora Overhaul Mods]
[Specific Smaller Flora Mods]
[Towns and City Texture mods]
[Armor Overhaul (big mods)]
[Weapon Overhaul (big mods)]
[All other smaller replacers of armor & weapons]
[SkyRe Main followed by all additions except Races]
[Lighting Mods (Realistic Lighting, ELFX, w/e)]
[Small lighting mods that replace a single thing like Better Torches]
[Weather Mods (CoT, etc)
[Water Mods]
[All player / NPC related changes to textures, faces, etc (big mods)]
[Changes to single NPC]
[Additional NPC's]
[All small player additions, like brows, eyes, etc]
[Animations, killmoves, no spinning death, etc]
[SkyRe_Races]
[Charater making Extended]
[All Custom Races]
[ReProccer]
[Reproccer Patches]
Installing lose files simply follow the same logic, install Big to Small ... mostly you can just say overwrite (conflict) when asked, and the good thing is - when there's conflict you can choose which side wins by overwriting or not, so more work but more customization as well. Just be careful... some .esp files rely on lose files to be there and to do something specific (especially Animations!) so overwriting lose files belonging to a mod that does something with them can have unexpected results. Those mods are mostly also listed as not compatible, but mostly it's something unclear as 'Not compatible with mods that try to modify the same objects' or 'Incompatible with mods that change the same image space' or 'Incompatible with mods that change the blabla.hkx file' instead of listing any major mods that are known to be incompatible.
HTH