If you're using FCOM Beta 8.9 or later, then see the New Standard Load-Order Guide.
If you are using FCOM Beta 8.8 or earlier, then keep reading this page.
There are way too many possible configurations for FCOM to detail them all, but the following guide should help with suggestions for some of the most common questions.
Installing Francesco's SI Options
One of the most frequent questions from players has been how to configure Francesco's Leveled Creatures-Items mod. The standard configuration doesn't gain much by using any of Fran's options, but you can get a lot out of Fran's recent additions for Shivering Isles. Francesco's 4.5 (or later) versions add some great changes to the SI expansion. If you have the SI expansion and you want to use Fran's changes there, you can do this with FCOM using these instructions.
The following configuration uses Francesco's changes for SI, but leaves OOO and MMM as the dominant mods in Cyrodiil.
During installation of Fran's mod, you should select the following Fran options:
Shivering Isles version
MOBS
Hardcore Loot
Separate files <- this is critical for the expanded SI config
Living Economy(optional)
Optional items add-on
Optional chance of stronger bosses
Optional chance of stronger enemies
optional chance of more enemies
Optional leveled guards
This will install the suggested files for Fran's SI changes.
Expanded Load-Order
You should place the Fran optional plugins very early in your load order, as described below in the expanded load-order list:
Francesco's leveled creatures-items mod.esm
Francesco's optional new items add-on.esm
Tamrielic Ingredients.esm (with optional support patch included in FCOM 8.1 or later)
Oscuro's_Oblivion_Overhaul.esm (only with FCOM 7.6 or later)
Mart's Monster Mod.esm
TamrielTravelers.esm (optional; requires TamrielTravelers4OOO.esp v1.3 and FCOM_TamrielTravelers.esp)
Unofficial Oblivion Patch.esp
Unofficial Shivering Isles Patch MOBS.esp (this is Fran's version of USIP)
Francesco's optional chance of stronger bosses.esp
Francesco's optional chance of stronger enemies.esp
Francesco's optional chance of more enemies.esp
Francesco's optional leveled guards.esp
Other baseline plugins, including weather & sound mods,
Official plugins, such as DLCSpellTomes.esp, etc. (except for Knights of the Nine, which should load later)
UOMP, the Unofficial Official Mod Patches. (only if you have official plugins; UOMP for Knights.esp goes later)
TNR - all.esp (Tamriel NPCs Revamped should be selected in your Bashed Patch config, but it does not actually need to be active)
Bob's Armory Oblivion.esp (optional)
Oblivion WarCry EV.esp (optional)
Oscuro's_Oblivion_Overhaul.esp
Mart's Monster Mod for FCOM.esp
Mart's Monster Mod - Official Patch 1.2 compatibility fix.esp (only with MMM 2.01 -- not MMM 3.0)
Mart's Monster Mod - Looting NPCs & Creatures.esp (optional)
Mart's Monster Mod - More Wilderness Life.esp (optional)
Mart's Monster Mod - Diverse Creature Skins.esp (optional)
Mart's Monster Mod - City Defences.esp (optional)
FCOM_BobItemReleveler.esp (only if you use Bob's Armory option)
FCOM_FranItemReleveler.esp
FCOM_OOOItemReleveler.esp
FCOM_WarCryItemReleveler.esp (only if you use WarCry option)
FCOM_OOOSpawnReleveler.esp
FCOM_MMMSpawnReleveler.esp
FCOM_FranSISpawnReleveler.esp (Beta 8.3 or later)
Mart's Monster Mod - Spawn Rates - Increased.esp* (place optional MMM overrides here)
Mart's Monster Mod - No Giants.esp* (place optional MMM overrides here)
FCOM_WarcryFactions.esp (only if you use WarCry option)
MOU - Option plugins (only if you use MMM and OOO: Unity plugins. Don't use MOU - Leveled Lists.esp)
Quest plugins & override plugins, including:
Knights.esp (Knights of the Nine official plugin needs to load after OOO)
Knights - Unofficial Patch.esp (only if you have Knights.esp)
Tamrielic_Ingredients_cOMbo.esp (with optional support patch included in FCOM 8.1 or later)
TamrielTravelers4OOO.esp (with optional support patch included in FCOM 8.4 or later)
FCOM Optional Add-On Patches (Use the load order detailed here. Beta 8.1 or later.)
OOO132RC3Hotfixes.esp
FCOM_Vampires.esp (beta 8.6 or later)
GFX_Initial_Glow-all.esp (beware of other, less-compatible no-glow mods)
Beautiful People.esp, other beauty packs, etc.
Bashed Patch, 0.esp (called "Bashed Lists, 0.esp" in older versions of Wrye Bash)
(*) Note that MMM plugins like Spawn Rates - Increased, Spawn Rates - Reduced, Spawn Rates - Moderate Increased, No Spiders, No Werewolves, No Slimes, No Beholdens, No Reavers, Extra Reavers, etc., can be used here. Load spawnrate changers before the "no" options! Also note that the names of these plugins changed in MMM 3.1 RC (previously they were called Increased Spawn Rate, Reduced Spawn Rate, etc.).
The MMM option files for No Carrion Rats, No Undead Rise, and More Wilderness Life are not based on spawn list changes, so they will not show up in the Levelers list (and should not be specified as Relevelers in older versions of WryeBash).
For more general load-order advice, check the Load Order Guide.
Bashed Patch
If you are using an old version of Wrye Bash (prior to 0.98), then check the Old Bash page for important details. If you have a recent version, then everything you need to know is already described in the step-by-step Bashed Patch guide on the main FCOM homepage.
Update Your Savegame
To get Fran's NPC changes to work on an existing savegame, you must use Wrye Bash to Import NPC Levels from each of the Fran mods first, then from OOO. So, just to be safe, you may want to import from Fran's base ESM, Fran's stronger bosses, Fran's stronger enemies, Fran's leveled guards and OOO, in that order. The main point here is that you want to make sure you get any changes Fran may have made to NPC enemies in SI, such as the Heretics, etc. You definitely need to import from Fran's leveled guards and OOO, but the others may not be necessary.
This configuration will give you Fran's changes for SI stuff and OOO changes for everything else.