I'm reposting this into its own thread so more people will see it, in case they didn't watch the warriors den yesterday.
When new gear is looted, it will get random perks right? It seems that some can only come with 1 perk even at high level which is kind of dumb, but this is relevant for below.
1. Equipped gear
For gear that is on your character, when the perk system rolls out it will be converted differently than inventory gear. For the set your character is wearing, (which I'm assuming is your 3 loadouts, or may only be your most recent loadout used) your upgrades will be converted into perk upgrades. If your gear has say 3 upgrade levels, then you will get 3 levels distributed between the 1 or two perks given to that piece. For the entire set you have equipped, they won't be given random perks, rather one or two perks will be chosen for the whole set. That way, you don't have to mess around with your gear to try to get an actual working set. If you have a fully maxed set on a character, at the start of marching fire that character's equipped set will start out with maxed out activated perks.
2. Inventory gear
For gear in your inventory, each piece is assigned random perks and the upgrade levels will just be traded in for perk leveling.