The reason not all mods are on workshop is not all players have the steam version so would have to buy it twice to do so. Nexus is a middle ground for all which is needed thanks to EGS and MS.
As for mods from nexus just unpack into MechWarrior 5 Mercenaries\MWMercs\Mods and activate in games menu once it boots. If no "mods" folder just create one.

Steam workshop mods will be in valves workshop folder if you grab any and will also need to be activated in games menu to work.
Both mod locations are compatible so no worries there you can use both.

Coming back to this discussion.

So I've [mostly] got Vortex to work with a handful of mods, but there's a handful of issues.

Firstly, I am somehow unable to change the mod deploy order. It shows me the order of the mods, but it's in such a nonsensical mish-mash and I can't do anything about it.
http://puu.sh/ISqh7.png The Vortex mods list.

Second, There's the ingame mods list. I am unable to deal with the load order there either, because there are certain conflicts between mods, despite their Nexus pages saying they are compatible.
https://puu.sh/ISqek.png
https://puu.sh/ISqeq.png

I had been dealing with a lot of frustration and troubleshooting today because some mods just up and decided to stop working, well into having played several hours with them enabled. Out of nowhere, the game would crash on startup because apparently one or two files were missing, without saying where I could find them. I found which mods they are via process of elimination and constantly deploying Vortex, and after updating and reinstalling them to no change, uninstalled them and now the game boots up.

Another issue I am dealing with is that on defense or warzone missions, one or two enemies would not spawn and I am softlocked into the mission, forcing me to restart the game and/or move to another system... which also has the same softlocking issue due to lack of enemy spawns. I would like to know which mod is responsible for this so I can deal with it and get back to actually enjoying the game.

Don't use votex, manually dl then extract in mods folder and activate in games mod menu once booted then restart and good to go.

Originally posted by Wayz:

Don't use votex, manually dl then extract in mods folder and activate in games mod menu once booted then restart and good to go.

All the mods I installed via Vortex were in the MW5 mods folder in steam. I installed the ones that didn't work via Vortex, and the game broke. Uninstalled those mods again via deleting their folders, and the game works.

Like I said don't use vortex, its superfluous with this title.

Originally posted by Wayz:

Like I said don't use vortex, its superfluous with this title.

Read my post again. The mods were already in the steam folder's mod directory. I installed the mods I wanted and the game broke. I deleted the folders and then it worked.
http://puu.sh/ISrnE.png

Well, sweet than as long as you are happy. Vortex does nothing for this title though, it is superfluous but keep using it if it mean that much to ya. The in game mod manager manages the the files no matter where you get your mods and it can also manage load order.

Originally posted by Wayz:

Well, sweet than as long as you are happy. Vortex does nothing for this title though, it is superfluous but keep using it if it mean that much to ya. The in game mod manager manages the the files no matter where you get your mods and it can also manage load order.

This is going nowhere.
What I'm trying to say is that the previous post, I didn't even use Vortex, I manually installed the mods, broke the game, and uninstalled said mods and the game works.

Also, the ingame mod manager does not manage load order at all. If there was a way, I'm somehow not seeing it.

Oh right sorry has been a while since I have used but load order is changed in the mods [mod.json) file.

Originally posted by Wayz:

Oh right sorry has been a while since I have used but load order is changed in the mods (mod.json) file.

This is precisely what I needed to hear, thank you.