So if I understand it right, you now have to use Skyrim Launcher to arrange mods?
If so, it is ridiculous that you can't resize the window!
What I did was to use BOSS to set the order method then copy that order (minus the extra bits that BOSS puts in it) to the plugins.txt file found in...
C:\Users\username\AppData\Local\Skyrim
then I checked that order through the official launcher but use the SKSE to then launch and play the game.
My plugins.txt file looks like this...
# This file is used by Skyrim to keep track of your downloaded content.
# Please do not modify this file.
GetArrowsBack80.esm
ShadowStriping Fix.esp
SMIM_Fixes.esp
Vampire Eyes Fix.esp
VampireInvisibleItemsFix.esp
Whiterun Market Fixes.esp
SoS - The Dungeons.esp
SoS - The Wilds.esp
RealisticWaterTextures.esp
Birds.esp
Cliffracers.esp
Deflect Arrows Perk Fix.esp
dD - Enhanced Blood Main.esp
Headbomb's Better Sorting - Ammo.esp
Headbomb's Better Sorting - Books.esp
Headbomb's Better Sorting - Food (Light Weight).esp
Headbomb's Better Sorting - Ingredients.esp
Headbomb's Better Sorting - Miscellaneous.esp
Headbomb's Better Sorting - Potions (Light Weight).esp
Headbomb's Better Sorting - Soul Gems (Ranked).esp
Headbomb's Better Sorting - Spells.esp
RabbitsPlus.esp
Real Wildlife Skyrim 0.1.esp
RiftenSmelter.esp
Tamriel Compendium.esp
TK_Clutter_Plants.esp
CrowdedCities.esp
Auto Unequip Arrows.esp
Mart's Savegame DeBloatifier.esp
Smithing Perks Overhaul - Balanced.esp
Weapons and Armor fixes.esp
Weapons and Armor fixes - Hacks.esp
Complete Crafting Overhaul - BS version.esp
EMHighviewCottage.esp
dD - Realistic Ragdoll Force - Realistic.esp
CityForestV2_6.esp
Jump85.esp
portal2mod.esp
For the time being I think that the above is one solution until NMM is adapted to control the load order again..?