Modding Mass Effect is special in that it's not drag and drop modding like most games these days.

Download ALOT into a separate folder, and use it to choose all the texture packs you wish to use.

Download the content mods you wish to use, into a content mods folder (when available, I recommend using the torrents).

Start up Mod Manager, and do a game backup.

Download the modding tools (Mod Manager + ALOT).

Install the game and all applicable DLC (all official DLC + multiplayer DLC recommended).

The initial process can take a long time - come prepared with a good book while you wait :)

The only way is to start over entirely, using a previous backup of the vanilla game (which can be done with the mods manager). Once the texture mods have been installed via ALOT, there is no going back to modify something, or add additional mods. Modding Mass Effect games can be considered a one-time process. DLCs are simply loose files bundled together, which makes them easier to install. Some mods come as loose files that have to be copied into the game folders, and others come as DLCs.

Texture mods (updated or new textures, sounds, video).

Content mods (new missions, armor, etc).

Mods can generally be split into two categories:

Gibbed's save editor (Editing save games).

ALOT installer* (Texture pack installer).

ME3Tweaks Mods manager* (Content mod installer).

While this may sound simple, a lot of care has to be taken when doing this, because Mass Effect 3 was not designed to be moddable. The basic pinciple is copying mod files into the game's CookedPCConsole folder, which contains the final files that the game uses. Collected notes on modding Mass Effect 3, as well as some helpful playing tips.

Mass effect 3 coalesced mod